COLLECTIVE VARIABLES MODULE

Reference manual for LAMMPS

Code version: 2018-11-16

Alejandro Bernardin, Jeffrey R. Comer, Giacomo Fiorin, Haohao Fu, Jérôme Hénin, Axel
Kohlmeyer, Fabrizio Marinelli, Joshua V. Vermaas, Andrew D. White
Contents
1 Overview 3

2 A crash course 4

3 General parameters 5
3.1 LAMMPS keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
3.2 Configuration syntax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
3.3 Global keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
3.4 Output files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

4 Defining collective variables 10

4.1 Choosing a function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
4.1.1 distance: center-of-mass distance between two groups. . . . . . . . . . . . . . . . 12
4.1.2 distanceZ: projection of a distance vector on an axis. . . . . . . . . . . . . . . . . 13
4.1.3 distanceXY: modulus of the projection of a distance vector on a plane. . . . . . . . 13
4.1.4 distanceVec: distance vector between two groups. . . . . . . . . . . . . . . . . . . 14
4.1.5 distanceDir: distance unit vector between two groups. . . . . . . . . . . . . . . . 14
4.1.6 distanceInv: mean distance between two groups of atoms. . . . . . . . . . . . . . 15
4.1.7 distancePairs: set of pairwise distances between two groups. . . . . . . . . . . . 15
4.1.8 cartesian: vector of atomic Cartesian coordinates. . . . . . . . . . . . . . . . . . 15
4.1.9 angle: angle between three groups. . . . . . . . . . . . . . . . . . . . . . . . . . . 16
4.1.10 dipoleAngle: angle between two groups and dipole of a third group. . . . . . . . . 16
4.1.11 dihedral: torsional angle between four groups. . . . . . . . . . . . . . . . . . . . . 16
4.1.12 polarTheta: polar angle in spherical coordinates. . . . . . . . . . . . . . . . . . . 17
4.1.13 polarPhi: azimuthal angle in spherical coordinates. . . . . . . . . . . . . . . . . . 17
4.1.14 coordNum: coordination number between two groups. . . . . . . . . . . . . . . . . . 17
4.1.15 selfCoordNum: coordination number between atoms within a group. . . . . . . . . 19
4.1.16 hBond: hydrogen bond between two atoms. . . . . . . . . . . . . . . . . . . . . . . 20
4.1.17 rmsd: root mean square displacement (RMSD) from reference positions. . . . . . . 20
4.1.18 Advanced usage of the rmsd component. . . . . . . . . . . . . . . . . . . . . . . . 21
4.1.19 eigenvector: projection of the atomic coordinates on a vector. . . . . . . . . . . . 22
4.1.20 gyration: radius of gyration of a group of atoms. . . . . . . . . . . . . . . . . . . 23
4.1.21 inertia: total moment of inertia of a group of atoms. . . . . . . . . . . . . . . . . 23
4.1.22 inertiaZ: total moment of inertia of a group of atoms around a chosen axis. . . . . 23
4.1.23 orientation: orientation from reference coordinates. . . . . . . . . . . . . . . . . 24
4.1.24 orientationAngle: angle of rotation from reference coordinates. . . . . . . . . . . 24
4.1.25 orientationProj: cosine of the angle of rotation from reference coordinates. . . . 25
4.1.26 spinAngle: angle of rotation around a given axis. . . . . . . . . . . . . . . . . . . . 25
4.1.27 tilt: cosine of the rotation orthogonal to a given axis. . . . . . . . . . . . . . . . . 25
4.2 Shared keywords for all components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
4.3 Periodic components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
4.4 Non-scalar components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
4.4.1 Calculating total forces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
4.5 Linear and polynomial combinations of components . . . . . . . . . . . . . . . . . . . . . . 28
4.6 Custom functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
4.7 Defining grid parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

1
 4.8 Trajectory output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
4.9 Extended Lagrangian . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
4.10 Backward-compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
4.11 Statistical analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

5 Selecting atoms 36
5.1 Atom selection keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
5.2 Moving frame of reference. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
5.3 Treatment of periodic boundary conditions. . . . . . . . . . . . . . . . . . . . . . . . . . . 40
5.4 Performance of a Colvars calculation based on group size. . . . . . . . . . . . . . . . . . . 40

6 Biasing and analysis methods 41

6.1 Adaptive Biasing Force . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
6.1.1 ABF requirements on collective variables . . . . . . . . . . . . . . . . . . . . . . . 43
6.1.2 Parameters for ABF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
6.1.3 Output files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
6.1.4 Post-processing: reconstructing a multidimensional free energy surface . . . . . . . 46
6.2 Extended-system Adaptive Biasing Force (eABF) . . . . . . . . . . . . . . . . . . . . . . . 47
6.2.1 CZAR estimator of the free energy . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
6.3 Metadynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
6.3.1 Basic syntax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
6.3.2 Output files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
6.3.3 Performance tuning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
6.3.4 Well-tempered metadynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
6.3.5 Multiple-replicas metadynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
6.3.6 Compatibility and post-processing . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
6.4 Harmonic restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
6.4.1 Moving restraints: steered molecular dynamics . . . . . . . . . . . . . . . . . . . . 54
6.4.2 Moving restraints: umbrella sampling . . . . . . . . . . . . . . . . . . . . . . . . . 55
6.4.3 Changing force constant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
6.5 Computing the work of a changing restraint . . . . . . . . . . . . . . . . . . . . . . . . . . 57
6.6 Harmonic wall restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
6.7 Linear restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
6.8 Adaptive Linear Bias/Experiment Directed Simulation . . . . . . . . . . . . . . . . . . . . 59
6.9 Multidimensional histograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
6.9.1 Grid definition for multidimensional histograms . . . . . . . . . . . . . . . . . . . . 62
6.10 Probability distribution-restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

7 Syntax changes from older versions 64

2
1 Overview
In molecular dynamics simulations, it is often useful to reduce the large number of degrees of freedom of a
physical system into few parameters whose statistical distributions can be analyzed individually, or used to
define biasing potentials to alter the dynamics of the system in a controlled manner. These have been called
‘order parameters’, ‘collective variables’, ‘(surrogate) reaction coordinates’, and many other terms.
Here we use primarily the term ‘collective variable’, often shortened to colvar, to indicate any differen-
tiable function of atomic Cartesian coordinates, xi , with i between 1 and N, the total number of atoms:

ξ (t) = ξ (X(t)) = ξ (xi (t), x j (t), xk (t), . . .) , 1 ≤ i, j, k . . . ≤ N (1)

This manual documents the collective variables module (Colvars), a software that provides an implemen-
tation for the functions ξ (X) with a focus on flexibility, robustness and high performance. The module is
designed to perform multiple tasks concurrently during or after a simulation, the most common of which
are:

• apply restraints or biasing potentials to multiple variables, tailored on the system by choosing from a
wide set of basis functions, without limitations on their number or on the number of atoms involved;

• calculate potentials of mean force (PMFs) along any set of variables, using different enhanced sam-
pling methods, such as Adaptive Biasing Force (ABF), metadynamics, steered MD and umbrella
sampling; variants of these methods that make use of an ensemble of replicas are supported as well;

• calculate statistical properties of the variables, such as running averages and standard deviations,
correlation functions of pairs of variables, and multidimensional histograms: this can be done either
at run-time without the need to save very large trajectory files, or after a simulation has been completed
using VMD and the cv command.

Detailed explanations of the design of the Colvars module are provided in reference [1]. Please cite this
reference whenever publishing work that makes use of this module.

3
2 A crash course
Suppose that we want to run a steered MD experiment where a small molecule is pulled away from a protein
binding site. In Colvars terms, this is done by applying a moving restraint to the distance between the two
objects. The configuration will contain two blocks, one defining the distance variable (see section 4 and
4.1.1), and the other the moving harmonic restraint (6.4).

colvar {
name dist
distance {
group1 { atomNumbersRange 42-55 }
group2 {
psfSegID PR
atomNameResidueRange CA 15-30 }
}
}
}

harmonic {
colvars dist
forceConstant 20.0
centers 4. # initial distance
targetCenters 15. # final distance
targetNumSteps 500000
}

Reading this input in plain English: the variable here named dist consists in a distance function between
the centers of two groups: the ligand (atoms 42 to 55) and the alpha carbon atoms (CA) of residues 15 to 30
in the protein (segment name PR). The atom selection syntax is detailed in section 5.
To the “dist” variable, we apply a harmonic potential of force constant 20 energy units/Å2 , initially
centered around a value of 4 Å, which will increase to 15 Å over 500,000 simulation steps.

4
3 General parameters
Here, we document the syntax of the commands and parameters used to set up and use the Colvars module
in LAMMPS. One of these parameters is the configuration file or the configuration text for the module itself,
whose syntax is described in 3.2 and in the following sections.

3.1 LAMMPS keywords

To enable a Colvars-based calculation, the following line must be added to the LAMMPS configuration file:

fix ID all colvars configfile keyword value pairs ...

where ID is a string that uniquely identifies this fix command inside a LAMMPS script, configfile is the
name of the configuration file for the Colvars module, followed by one or more of the following optional
keywords with their corresponding arguments:

• input h Name or prefix of the input state file i

Context: Keyword of the fix colvars command
Acceptable values: string
Description: If a value is provided, it is interpreted as either the name of the input state file, or as the
prefix of the file named input.colvars.state. This file contains information needed to continue a
previous collective variables-based calculation, including the number of the last computed step (useful
for time-dependent biases). The same information is also stored in the binary restart files written by
LAMMPS, so this option is not needed when continuing a calculation from a LAMMPS restart.

• output h Prefix of the output state file i

Context: Keyword of the fix colvars command
Acceptable values: string
Default value: “out”
Description: If a value is provided, it is interpreted as the prefix to all output files that will be written
by the Colvars module (see 3.4).

• unwrap h Whether to unwrap coordinates passed to the Colvars module i

Context: keyword of the fix colvars command
Acceptable values: “yes” or “no”
Default value: “yes”
Description: This keyword controls whether wrapped or unwrapped coordinates are passed to the
Colvars module for calculation of the collective variables and of the resulting forces. The default is
to use the image flags to reconstruct the absolute atom positions: under this convention, centers of
mass and centers of geometry are calculated as a weighted vector sum (see 5.3). Setting this to no will
use the current local coordinates that are wrapped back into the simulation cell at each re-neighboring
instead.

• seed h Seed for the random number generator i

Context: Keyword of the fix colvars command
Acceptable values: positive integer
Default value: 1966

5
 Description: If defined, the value of this keyword is provided as seed to the random number genera-
tor. This is only meaningful when the extendedLangevinDamping keyword is used (see 4.9).

• tstat h Thermostating fix i

Context: Keyword of the fix colvars command
Acceptable values: string
Default value: NULL
Description: This keyword provides the ID of an applicable thermostating fix command. This will
be used to provide the Colvars module with the current thermostat target temperature when using a
method that needs this information.

3.2 Configuration syntax

The syntax of the Colvars configuration is “keyword value”, where the keyword and its value are separated
by any white space. The following rules apply:

• keywords are case-insensitive (upperBoundary is the same as upperboundary and UPPERBOUNDARY):

their string values are however case-sensitive (e.g. file names);

• a long value or a list of multiple values can be distributed across multiple lines by using curly braces,
“{” and “}”: the opening brace “{” must occur on the same line as the keyword, following a space
character or other white space; the closing brace “}” can be at any position after that;

• many keywords are nested, and are only meaningful within a specific context: for every keyword
documented in the following, the “parent” keyword that defines such context is also indicated;

• if a keyword requiring a boolean value (yes|on|true or no|off|false) is provided without an ex-

plicit value, it defaults to ‘yes|on|true’; for example, ‘outputAppliedForce’ may be used as short-
hand for ‘outputAppliedForce on’;

• the hash character # indicates a comment: all text in the same line following this character will be
ignored.

3.3 Global keywords

The following keywords are available in the global context of the Colvars configuration, i.e. they are not
nested inside other keywords:

• colvarsTrajFrequency h Colvar value trajectory frequency i

Context: global
Acceptable values: positive integer
Default value: 100
Description: The values of each colvar (and of other related quantities, if requested) are written to
the file output.colvars.traj every these many steps throughout the simulation. If the value is 0,
such trajectory file is not written. For optimization the output is buffered, and synchronized with the
disk only when the restart file is being written.

6
 • colvarsRestartFrequency h Colvar module restart frequency i
Context: global
Acceptable values: positive integer
Default value: restartFreq
Description: Allows to choose a different restart frequency for the Colvars module. Redefining it
may be useful to trace the time evolution of those few properties which are not written to the trajectory
file for reasons of disk space.

• indexFile h Index file for atom selection (GROMACS “ndx” format) i

Context: global
Acceptable values: UNIX filename
Description: This option reads an index file (usually with a .ndx extension) as produced by the
make ndx tool of GROMACS. This keyword may be repeated to load multiple index files: the same
group name cannot appear in multiple index files. In LAMMPS, the group2ndx command can be
used to generate such file from existing groups. Note that the Colvars module reads the indices of
atoms from the index file: therefore, the LAMMPS groups do not need to remain active during the
simulation, and could be deleted right after issuing group2ndx. The names of index groups contained
in this file can then be used to define atom groups with the indexGroup keyword. Other supported
methods to select atoms are described in 5.

• smp h Whether SMP parallelism should be used i

Context: global
Acceptable values: boolean
Default value: on
Description: If this flag is enabled (default), SMP parallelism over threads will be used to compute
variables and biases, provided that this is supported by the LAMMPS build in use.

To illustrate the flexibility of the Colvars module, a non-trivial setup is represented in Figure 1. The
corresponding configuration is given below. The options within the colvar blocks are described in 4, those
within the harmonic and histogram blocks in 6. Note: except colvar, none of the keywords shown is
mandatory.

colvar {
# difference of two distances
name d
width 0.2 # 0.2 Å of estimated fluctuation width
distance {
componentCoeff 1.0
group1 { atomNumbers 1 2 }
group2 { atomNumbers 3 4 5 }
}
distance {
componentCoeff -1.0
group1 { atomNumbers 7 }
group2 { atomNumbers 8 9 10 }
}
}

colvar {

7
Figure 1: Graphical representation of a Colvars configuration (note: currently, the α-helical content colvar
is unavailable in LAMMPS). The colvar called “d” is defined as the difference between two distances: the
first distance (d1 ) is taken between the center of mass of atoms 1 and 2 and that of atoms 3 to 5, the second
(d2 ) between atom 7 and the center of mass of atoms 8 to 10. The difference d = d1 − d2 is obtained
by multiplying the two by a coefficient C = +1 or C = −1, respectively. The colvar called “c” is the
coordination number calculated between atoms 1 to 10 and atoms 11 to 20. A harmonic restraint is applied
to both d and c: to allow using the same force constant K, both d and c are scaled by their respective
fluctuation widths wd and wc . The values of “c” are also recorded throughout the simulation as a joint
2-dimensional histogram.

name c
coordNum {
cutoff 6.0
group1 { atomNumbersRange 1-10 }
group2 { atomNumbersRange 11-20 }
}
}

harmonic {
colvars d c
centers 3.0 4.0
forceConstant 5.0
}

histogram {
colvars c
}

8
 Section 4 explains how to define a colvar and its behavior, regardless of its specific functional form. To
define colvars that are appropriate to a specific physical system, Section 5 documents how to select atoms,
and section 4 lists all of the available functional forms, which we call “colvar components”. Finally, section
6 lists the available methods and algorithms to perform biased simulations and multidimensional analysis of
colvars.

3.4 Output files

During a simulation with collective variables defined, the following three output files are written:

• A state file, named output.colvars.state; this file is in ASCII (plain text) format. This file is written
at the end of the specified run.
This is the only Colvars output file needed to continue a simulation.

• If the parameter colvarsRestartFrequency is larger than zero, a restart file is written every that
many steps: this file is fully equivalent to the final state file. The name of this file is restart.colvars.state.

• If the parameter colvarsTrajFrequency is greater than 0 (default: 100), a trajectory file is written
during the simulation: its name is output.colvars.traj; unlike the state file, it is not needed to
restart a simulation, but can be used later for post-processing and analysis.

Other output files may also be written by specific methods, e.g. the ABF or metadynamics methods (6.1,
6.3). Like the trajectory file, they are needed only for analyzing, not continuing a simulation. All such files’
names also begin with the prefix output.

9
4 Defining collective variables
A collective variable is defined by the keyword colvar followed by its configuration options contained
within curly braces:

colvar {
name xi
<other options>
function name {
<parameters>
<atom selection>
}
}

There are multiple ways of defining a variable:

• The simplest and most common way way is using one of the precompiled functions (here called “com-
ponents”), which are listed in section 4.1. For example, using the keyword rmsd (section 4.1.17)
defines the variable as the root mean squared deviation (RMSD) of the selected atoms.

• A new variable may also be constructed as a linear or polynomial combination of the components
listed in section 4.1 (see 4.5 for details).

• A user-defined mathematical function of the existing components (see list in section 4.1), or of the
atomic coordinates directly (see the cartesian keyword in 4.1.8). The function is defined through
the keyword customFunction (see 4.6 for details).

Choosing a component (function) is the only parameter strictly required to define a collective variable. It is
also highly recommended to specify a name for the variable:

• name h Name of this colvar i

Context: colvar
Acceptable values: string
Default value: “colvar” + numeric id
Description: The name is an unique case-sensitive string which allows the Colvars module to identify
this colvar unambiguously; it is also used in the trajectory file to label to the columns corresponding
to this colvar.

4.1 Choosing a function

In this context, the function that computes a colvar is called a component. A component’s choice and
definition consists of including in the variable’s configuration a keyword indicating the type of function (e.g.
rmsd), followed by a definition block specifying the atoms involved (see 5) and any additional parameters
(cutoffs, “reference” values, . . . ). At least one component must be chosen to define a variable: if none of the
keywords listed below is found, an error is raised.
The following components implement functions with a scalar value (i.e. a real number):

10
• distance: distance between two groups;

• distanceZ: projection of a distance vector on an axis;

• distanceXY: projection of a distance vector on a plane;

• distanceInv: mean distance between two groups of atoms (e.g. NOE-based distance);

• angle: angle between three groups;

• dihedral: torsional (dihedral) angle between four groups;

• dipoleAngle: angle between two groups and dipole of a third group;

• polarTheta: polar angle of a group in spherical coordinates;

• polarPhi: azimuthal angle of a group in spherical coordinates;

• coordNum: coordination number between two groups;

• selfCoordNum: coordination number of atoms within a group;

• hBond: hydrogen bond between two atoms;

• rmsd: root mean square deviation (RMSD) from a set of reference coordinates;

• eigenvector: projection of the atomic coordinates on a vector;

• orientationAngle: angle of the best-fit rotation from a set of reference coordinates;

• orientationProj: cosine of orientationProj;

• spinAngle: projection orthogonal to an axis of the best-fit rotation from a set of reference coordinates;

• tilt: projection on an axis of the best-fit rotation from a set of reference coordinates;

• gyration: radius of gyration of a group of atoms;

• inertia: moment of inertia of a group of atoms;

• inertiaZ: moment of inertia of a group of atoms around a chosen axis;

Some components do not return scalar, but vector values:

• distanceVec: distance vector between two groups (length: 3);

• distanceDir: unit vector parallel to distanceVec (length: 3);

• cartesian: vector of atomic Cartesian coordinates (length: N times the number of Cartesian compo-
nents requested, X, Y or Z);

• distancePairs: vector of mutual distances (length: N1 × N2 );

• orientation: best-fit rotation, expressed as a unit quaternion (length: 4).

11
 The types of components used in a colvar (scalar or not) determine the properties of that colvar, and
particularly which biasing or analysis methods can be applied.
What if “X” is not listed? If a function type is not available on this list, it may be possible to define it
as a polynomial superposition of existing ones (see 4.5), a custom function (see 4.6).
In the rest of this section, all available component types are listed, along with their physical units and the
ranges of values, if limited. Such limiting values can be used to define lowerBoundary and upperBoundary
in the parent colvar.
For each type of component, the available configurations keywords are listed: when two components
share certain keywords, the second component references to the documentation of the first one that uses
that keyword. The very few keywords that are available for all types of components are listed in a separate
section 4.2.

4.1.1 distance: center-of-mass distance between two groups.

The distance {...} block defines a distance component between the two atom groups, group1 and
group2.
List of keywords (see also 4.5 for additional options):

• group1 h First group of atoms i

Context: distance
Acceptable values: Block group1 {...}
Description: First group of atoms.

• group2: analogous to group1

• forceNoPBC h Calculate absolute rather than minimum-image distance? i

Context: distance
Acceptable values: boolean
Default value: no
Description: By default, in calculations with periodic boundary conditions, the distance compo-
nent returns the distance according to the minimum-image convention. If this parameter is set to yes,
PBC will be ignored and the distance between the coordinates as maintained internally will be used.
This is only useful in a limited number of special cases, e.g. to describe the distance between remote
points of a single macromolecule, which cannot be split across periodic cell boundaries, and for which
the minimum-image distance might give the wrong result because of a relatively small periodic cell.

• oneSiteTotalForce h Measure total force on group 1 only? i

Context: angle, dipoleAngle, dihedral
Acceptable values: boolean
Default value: no
Description: If this is set to yes, the total force is measured along a vector field (see equation (15) in
section 6.1) that only involves atoms of group1. This option is only useful for ABF, or custom biases
that compute total forces. See section 6.1 for details.

The value returned is a positive number (in Å), ranging from 0 to the largest possible interatomic distance
within the chosen boundary conditions (with PBCs, the minimum image convention is used unless the
forceNoPBC option is set).

12
4.1.2 distanceZ: projection of a distance vector on an axis.
The distanceZ {...} block defines a distance projection component, which can be seen as measuring the
distance between two groups projected onto an axis, or the position of a group along such an axis. The
axis can be defined using either one reference group and a constant vector, or dynamically based on two
reference groups. One of the groups can be set to a dummy atom to allow the use of an absolute Cartesian
coordinate.
List of keywords (see also 4.5 for additional options):

• main h Main group of atoms i

Context: distanceZ
Acceptable values: Block main {...}
Description: Group of atoms whose position r is measured.

• ref h Reference group of atoms i

Context: distanceZ
Acceptable values: Block ref {...}
Description: Reference group of atoms. The position of its center of mass is noted r1 below.

• ref2 h Secondary reference group i

Context: distanceZ
Acceptable values: Block ref2 {...}
Default value: none
Description: Optional group of reference atoms, whose position r2 can be used to define a dynamic
projection axis: e = (kr2 − r1 k)−1 × (r2 − r1 ). In this case, the origin is rm = 1/2(r1 + r2 ), and the
value of the component is e · (r − rm ).

• axis h Projection axis (Å) i

Context: distanceZ
Acceptable values: (x, y, z) triplet
Default value: (0.0, 0.0, 1.0)
Description: The three components of this vector define a projection axis e for the distance vector
r − r1 joining the centers of groups ref and main. The value of the component is then e · (r − r1 ). The
vector should be written as three components separated by commas and enclosed in parentheses.

• forceNoPBC: see definition of forceNoPBC in sec. 4.1.1 (distance component)

• oneSiteTotalForce: see definition of oneSiteTotalForce in sec. 4.1.1 (distance component)

This component returns a number (in Å) whose range is determined by the chosen boundary conditions. For
instance, if the z axis is used in a simulation with periodic boundaries, the returned value ranges between
−bz /2 and bz /2, where bz is the box length along z (this behavior is disabled if forceNoPBC is set).

4.1.3 distanceXY: modulus of the projection of a distance vector on a plane.

The distanceXY {...} block defines a distance projected on a plane, and accepts the same keywords as
the component distanceZ, i.e. main, ref, either ref2 or axis, and oneSiteTotalForce. It returns the
norm of the projection of the distance vector between main and ref onto the plane orthogonal to the axis.
The axis is defined using the axis parameter or as the vector joining ref and ref2 (see distanceZ above).
List of keywords (see also 4.5 for additional options):

13
 • main: see definition of main in sec. 4.1.2 (distanceZ component)

• ref: see definition of ref in sec. 4.1.2 (distanceZ component)

• ref2: see definition of ref2 in sec. 4.1.2 (distanceZ component)

• axis: see definition of axis in sec. 4.1.2 (distanceZ component)

• forceNoPBC: see definition of forceNoPBC in sec. 4.1.1 (distance component)

• oneSiteTotalForce: see definition of oneSiteTotalForce in sec. 4.1.1 (distance component)

4.1.4 distanceVec: distance vector between two groups.

The distanceVec {...} block defines a distance vector component, which accepts the same keywords as
the component distance: group1, group2, and forceNoPBC. Its value is the 3-vector joining the centers of
mass of group1 and group2.
List of keywords (see also 4.5 for additional options):

• group1: see definition of group1 in sec. 4.1.1 (distance component)

• group2: analogous to group1

• forceNoPBC: see definition of forceNoPBC in sec. 4.1.1 (distance component)

• oneSiteTotalForce: see definition of oneSiteTotalForce in sec. 4.1.1 (distance component)

4.1.5 distanceDir: distance unit vector between two groups.

The distanceDir {...} block defines a distance unit vector component, which accepts the same keywords
as the component distance: group1, group2, and forceNoPBC. It returns a 3-dimensional unit vector
d = (dx , dy , dz ), with |d| = 1.
List of keywords (see also 4.5 for additional options):

• group1: see definition of group1 in sec. 4.1.1 (distance component)

• group2: analogous to group1

• forceNoPBC: see definition of forceNoPBC in sec. 4.1.1 (distance component)

• oneSiteTotalForce: see definition of oneSiteTotalForce in sec. 4.1.1 (distance component)

14
4.1.6 distanceInv: mean distance between two groups of atoms.
The distanceInv {...} block defines a generalized mean distance between two groups of atoms 1 and 2,
weighted with exponent 1/n:
 n !−1/n
[n] 1 1
d1,2 = (2)
N1 N2 ∑i, j kdi j k

where kdi j k is the distance between atoms i and j in groups 1 and 2 respectively, and n is an even integer.
List of keywords (see also 4.5 for additional options):

• group1: see definition of group1 in sec. 4.1.1 (distance component)

• group2: analogous to group1

• oneSiteTotalForce: see definition of oneSiteTotalForce in sec. 4.1.1 (distance component)

• exponent h Exponent n in equation 2 i

Context: distanceInv
Acceptable values: positive even integer
Default value: 6
Description: Defines the exponent to which the individual distances are elevated before averaging.
The default value of 6 is useful for example to applying restraints based on NOE-measured distances.

This component returns a number in Å, ranging from 0 to the largest possible distance within the chosen
boundary conditions.

4.1.7 distancePairs: set of pairwise distances between two groups.

The distancePairs {...} block defines a N1 × N2 -dimensional variable that includes all mutual distances
between the atoms of two groups. This can be useful, for example, to develop a new variable defined over
two groups, by using the scriptedFunction feature.
List of keywords (see also 4.5 for additional options):

• group1: see definition of group1 in sec. 4.1.1 (distance component)

• group2: analogous to group1

• forceNoPBC: see definition of forceNoPBC in sec. 4.1.1 (distance component)

This component returns a N1 ×N2 -dimensional vector of numbers, each ranging from 0 to the largest possible
distance within the chosen boundary conditions.

4.1.8 cartesian: vector of atomic Cartesian coordinates.

The cartesian {...} block defines a component returning a flat vector containing the Cartesian coordi-
nates of all participating atoms, in the order (x1 , y1 , z1 , · · · , xn , yn , zn ).
List of keywords (see also 4.5 for additional options):

15
 • atoms h Group of atoms i
Context: cartesian
Acceptable values: Block atoms {...}
Description: Defines the atoms whose coordinates make up the value of the component. If rotateReference
or centerReference are defined, coordinates are evaluated within the moving frame of reference.

4.1.9 angle: angle between three groups.

The angle {...} block defines an angle, and contains the three blocks group1, group2 and group3,
defining the three groups. It returns an angle (in degrees) within the interval [0 : 180].
List of keywords (see also 4.5 for additional options):

• group1: see definition of group1 in sec. 4.1.1 (distance component)

• group2: analogous to group1

• group3: analogous to group1

• forceNoPBC: see definition of forceNoPBC in sec. 4.1.1 (distance component)

• oneSiteTotalForce: see definition of oneSiteTotalForce in sec. 4.1.1 (distance component)

4.1.10 dipoleAngle: angle between two groups and dipole of a third group.
The dipoleAngle {...} block defines an angle, and contains the three blocks group1, group2 and group3,
defining the three groups, being group1 the group where dipole is calculated. It returns an angle (in degrees)
within the interval [0 : 180].
List of keywords (see also 4.5 for additional options):

• group1: see definition of group1 in sec. 4.1.1 (distance component)

• group2: analogous to group1

• group3: analogous to group1

• forceNoPBC: see definition of forceNoPBC in sec. 4.1.1 (distance component)

• oneSiteTotalForce: see definition of oneSiteTotalForce in sec. 4.1.1 (distance component)

4.1.11 dihedral: torsional angle between four groups.

The dihedral {...} block defines a torsional angle, and contains the blocks group1, group2, group3
and group4, defining the four groups. It returns an angle (in degrees) within the interval [−180 : 180]. The
Colvars module calculates all the distances between two angles taking into account periodicity. For instance,
reference values for restraints or range boundaries can be defined by using any real number of choice.
List of keywords (see also 4.5 for additional options):

• group1: see definition of group1 in sec. 4.1.1 (distance component)

16
 • group2: analogous to group1

• group3: analogous to group1

• group4: analogous to group1

• forceNoPBC: see definition of forceNoPBC in sec. 4.1.1 (distance component)

• oneSiteTotalForce: see definition of oneSiteTotalForce in sec. 4.1.1 (distance component)

4.1.12 polarTheta: polar angle in spherical coordinates.

The polarTheta {...} block defines the polar angle in spherical coordinates, for the center of mass of a
group of atoms described by the block atoms. It returns an angle (in degrees) within the interval [0 : 180]. To
obtain spherical coordinates in a frame of reference tied to another group of atoms, use the fittingGroup
(5.2) option within the atoms block. An example is provided in file examples/11 polar angles.in of the
Colvars public repository.
List of keywords (see also 4.5 for additional options):

• atoms h Atom group i

Context: polarPhi
Acceptable values: atoms {...} block
Description: Defines the group of atoms for the COM of which the angle should be calculated.

4.1.13 polarPhi: azimuthal angle in spherical coordinates.

The polarPhi {...} block defines the azimuthal angle in spherical coordinates, for the center of mass of a
group of atoms described by the block atoms. It returns an angle (in degrees) within the interval [−180 : 180].
The Colvars module calculates all the distances between two angles taking into account periodicity. For in-
stance, reference values for restraints or range boundaries can be defined by using any real number of choice.
To obtain spherical coordinates in a frame of reference tied to another group of atoms, use the fittingGroup
(5.2) option within the atoms block. An example is provided in file examples/11 polar angles.in of the
Colvars public repository.
List of keywords (see also 4.5 for additional options):

• atoms h Atom group i

Context: polarPhi
Acceptable values: atoms {...} block
Description: Defines the group of atoms for the COM of which the angle should be calculated.

4.1.14 coordNum: coordination number between two groups.

The coordNum {...} block defines a coordination number (or number of contacts), which calculates the
function (1 − (d/d0 )n )/(1 − (d/d0 )m ), where d0 is the “cutoff” distance, and n and m are exponents that can

17
control its long range behavior and stiffness [2]. This function is summed over all pairs of atoms in group1
and group2:
1 − (|xi − x j |/d0 )n
C(group1, group2) = ∑ ∑ m
(3)
i∈group1 j∈group2 1 − (|xi − x j |/d0 )

List of keywords (see also 4.5 for additional options):

• group1: see definition of group1 in sec. 4.1.1 (distance component)

• group2: analogous to group1

• cutoff h “Interaction” distance (Å) i

Context: coordNum
Acceptable values: positive decimal
Default value: 4.0
Description: This number defines the switching distance to define an interatomic contact: for d  d0 ,
the switching function (1 − (d/d0 )n )/(1 − (d/d0 )m ) is close to 1, at d = d0 it has a value of n/m (1/2
with the default n and m), and at d  d0 it goes to zero approximately like d m−n . Hence, for a proper
behavior, m must be larger than n.

• cutoff3 h Reference distance vector (Å) i

Context: coordNum
Acceptable values: “(x, y, z)” triplet of positive decimals
Default value: (4.0, 4.0, 4.0)
Description: The three components of this vector define three different cutoffs d0 for each direction.
This option is mutually exclusive with cutoff.

• expNumer h Numerator exponent i

Context: coordNum
Acceptable values: positive even integer
Default value: 6
Description: This number defines the n exponent for the switching function.

• expDenom h Denominator exponent i

Context: coordNum
Acceptable values: positive even integer
Default value: 12
Description: This number defines the m exponent for the switching function.

• group2CenterOnly h Use only group2’s center of mass i

Context: coordNum
Acceptable values: boolean
Default value: off
Description: If this option is on, only contacts between each atoms in group1 and the center of mass
of group2 are calculated (by default, the sum extends over all pairs of atoms in group1 and group2).
If group2 is a dummyAtom, this option is set to yes by default.

• tolerance h Pairlist control i

Context: coordNum
Acceptable values: decimal
Default value: 0.0

18
 Description: This controls the pairlist feature, dictating the minimum value for each summation
element in Eq. 3 such that the pair that contributed the summation element is included in subsequent
simulation timesteps until the next pairlist recalculation. For most applications, this value should be
small (eg. 0.001) to avoid missing important contributions to the overall sum. Higher values will
improve performance by reducing the number of pairs that contribute to the sum. Values above 1
will exclude all possible pair interactions. Similarly, values below 0 will never exclude a pair from
consideration. To ensure continuous forces, Eq. 3 is further modified by subtracting the tolerance and
then rescaling so that each pair covers the range [0, 1].
• pairListFrequency h Pairlist regeneration frequency i
Context: coordNum
Acceptable values: positive integer
Default value: 100
Description: This controls the pairlist feature, dictating how many steps are taken between regener-
ating pairlists if the tolerance is greater than 0.
This component returns a dimensionless number, which ranges from approximately 0 (all interatomic
distances are much larger than the cutoff) to Ngroup1 × Ngroup2 (all distances are less than the cutoff), or
Ngroup1 if group2CenterOnly is used. For performance reasons, at least one of group1 and group2 should
be of limited size or group2CenterOnly should be used: the cost of the loop over all pairs grows as
Ngroup1 × Ngroup2 . Setting tolerance > 0 ameliorates this to some degree, although every pair is still
checked to regenerate the pairlist.

4.1.15 selfCoordNum: coordination number between atoms within a group.

The selfCoordNum {...} block defines a coordination number similarly to the component coordNum, but
the function is summed over atom pairs within group1:
1 − (|xi − x j |/d0 )n
C(group1) = ∑ ∑ 1 − (|xi − x j |/d0 )m (4)
i∈group1 j>i

The keywords accepted by selfCoordNum are a subset of those accepted by coordNum, namely group1 (here
defining all of the atoms to be considered), cutoff, expNumer, and expDenom.
List of keywords (see also 4.5 for additional options):
• group1: see definition of group1 in sec. 4.1.14 (coordNum component)
• cutoff: see definition of cutoff in sec. 4.1.14 (coordNum component)
• cutoff3: see definition of cutoff3 in sec. 4.1.14 (coordNum component)
• expNumer: see definition of expNumer in sec. 4.1.14 (coordNum component)
• expDenom: see definition of expDenom in sec. 4.1.14 (coordNum component)
• tolerance: see definition of tolerance in sec. 4.1.14 (coordNum component)
• pairListFrequency: see definition of pairListFrequency in sec. 4.1.14 (coordNum component)
This component returns a dimensionless number, which ranges from approximately 0 (all interatomic
distances much larger than the cutoff) to Ngroup1 × (Ngroup1 − 1)/2 (all distances within the cutoff). For
performance reasons, group1 should be of limited size, because the cost of the loop over all pairs grows as
2
Ngroup1 .

19
4.1.16 hBond: hydrogen bond between two atoms.
The hBond {...} block defines a hydrogen bond, implemented as a coordination number (eq. 3) between
the donor and the acceptor atoms. Therefore, it accepts the same options cutoff (with a different default
value of 3.3 Å), expNumer (with a default value of 6) and expDenom (with a default value of 8). Unlike
coordNum, it requires two atom numbers, acceptor and donor, to be defined. It returns an adimensional
number, with values between 0 (acceptor and donor far outside the cutoff distance) and 1 (acceptor and
donor much closer than the cutoff).
List of keywords (see also 4.5 for additional options):

• acceptor h Number of the acceptor atom i

Context: hBond
Acceptable values: positive integer
Description: Number that uses the same convention as atomNumbers.

• donor: analogous to acceptor

• cutoff: see definition of cutoff in sec. 4.1.14 (coordNum component)

Note: default value is 3.3 Å.

• expNumer: see definition of expNumer in sec. 4.1.14 (coordNum component)

Note: default value is 6.

• expDenom: see definition of expDenom in sec. 4.1.14 (coordNum component)

Note: default value is 8.

4.1.17 rmsd: root mean square displacement (RMSD) from reference positions.
The block rmsd {...} defines the root mean square replacement (RMSD) of a group of atoms with respect
to a reference structure. For each set of coordinates {x1 (t), x2 (t), . . . xN (t)}, the colvar component rmsd
(ref)
calculates the optimal rotation U {xi (t)}→{xi } that best superimposes the coordinates {xi (t)} onto a set of
(ref)
reference coordinates {xi }. Both the current and the reference coordinates are centered on their centers
(ref)
of geometry, xcog (t) and xcog . The root mean square displacement is then defined as:
s
(ref) 1 N 
 (ref) (ref) 2

RMSD({xi (t)}, {xi }) = ∑ U xi (t) − xcog (t) − xi − xcog  (5)
N i=1
(ref)
The optimal rotation U {xi (t)}→{xi } is calculated within the formalism developed in reference [3], which
(ref)
guarantees a continuous dependence of U {xi (t)}→{xi } with respect to {xi (t)}.
List of keywords (see also 4.5 for additional options):

• atoms h Atom group i

Context: rmsd
Acceptable values: atoms {...} block
Description: Defines the group of atoms of which the RMSD should be calculated. Optimal fit op-
tions (such as refPositions and rotateReference) should typically NOT be set within this block.
Exceptions to this rule are the special cases discussed in the Advanced usage paragraph below.

20
 • refPositions h Reference coordinates i
Context: rmsd
Acceptable values: space-separated list of (x, y, z) triplets
Description: This option (mutually exclusive with refPositionsFile) sets the reference coordi-
nates for RMSD calculation, and uses these to compute the roto-translational fit. It is functionally
equivalent to the option refPositions in the atom group definition, which also supports more ad-
vanced fitting options.

• refPositionsFile h Reference coordinates file i

Context: rmsd
Acceptable values: UNIX filename
Description: This option (mutually exclusive with refPositions) sets the reference coordinates for
RMSD calculation, and uses these to compute the roto-translational fit. It is functionally equivalent
to the option refPositionsFile in the atom group definition, which also supports more advanced
fitting options.

This component returns a positive real number (in Å).

4.1.18 Advanced usage of the rmsd component.

In the standard usage as described above, the rmsd component calculates a minimum RMSD, that is, current
coordinates are optimally fitted onto the same reference coordinates that are used to compute the RMSD
value. The fit itself is handled by the atom group object, whose parameters are automatically set by the rmsd
component. For very specific applications, however, it may be useful to control the fitting process separately
from the definition of the reference coordinates, to evaluate various types of non-minimal RMSD values.
This can be achieved by setting the related options (refPositions, etc.) explicitly in the atom group block.
This allows for the following non-standard cases:

1. applying the optimal translation, but no rotation (rotateReference off), to bias or restrain the shape
and orientation, but not the position of the atom group;

2. applying the optimal rotation, but no translation (translateReference off), to bias or restrain the
shape and position, but not the orientation of the atom group;

3. disabling the application of optimal roto-translations, which lets the RMSD component decribe the
deviation of atoms from fixed positions in the laboratory frame: this allows for custom positional
restraints within the Colvars module;

4. fitting the atomic positions to different reference coordinates than those used in the RMSD calculation
itself;

5. applying the optimal rotation and/or translation from a separate atom group, defined through fittingGroup:
the RMSD then reflects the deviation from reference coordinates in a separate, moving reference
frame.

21
4.1.19 eigenvector: projection of the atomic coordinates on a vector.
The block eigenvector {...} defines the projection of the coordinates of a group of atoms (or more
precisely, their deviations from the reference coordinates) onto a vector in R3n , where n is the number of
atoms in the group. The computed quantity is the total projection:
n  
(ref) (ref) (ref)
p({xi (t)}, {xi }) = ∑ vi · U(xi (t) − xcog (t)) − (xi − xcog ) , (6)
i=1

(ref)
where, as in the rmsd component, U is the optimal rotation matrix, xcog (t) and xcog are the centers of
geometry of the current and reference positions respectively, and vi are the components of the vector for
each atom. Example choices for (vi ) are an eigenvector of the covariance matrix (essential mode), or a
normal mode of the system. It is assumed that ∑i vi = 0: otherwise, the Colvars module centers the vi
automatically when reading them from the configuration.
List of keywords (see also 4.5 for additional options):

• atoms: see definition of atoms in sec. 4.1.17 (rmsd component)

• refPositions: see definition of refPositions in sec. 4.1.17 (rmsd component)

• refPositionsFile: see definition of refPositionsFile in sec. 4.1.17 (rmsd component)

• vector h Vector components i

Context: eigenvector
Acceptable values: space-separated list of (x, y, z) triplets
Description: This option (mutually exclusive with vectorFile) sets the values of the vector com-
ponents.

• vectorFile h file containing vector components i

Context: eigenvector
Acceptable values: UNIX filename
Description: This option (mutually exclusive with vector) sets the name of a coordinate file contain-
ing the vector components; the file is read according to the same format used for refPositionsFile.

• differenceVector h The 3n-dimensional vector is the difference between vector and refPositions i
Context: eigenvector
Acceptable values: boolean
Default value: off
Description: If this option is on, the numbers provided
 by vector
 are interpreted as another set of
0 0 (ref)
positions, xi : the vector vi is then defined as vi = xi − xi . This allows to conveniently define a
colvar ξ as a projection on the linear transformation between two sets of positions, “A” and “B”. For
convenience, the vector is also normalized so that ξ = 0 when the atoms are at the set of positions “A”
and ξ = 1 at the set of positions “B”.

This component returns a number (in Å), whose value ranges between the smallest and largest absolute
positions in the unit cell during the simulations (see also distanceZ). Due to the normalization in eq. 6, this
range does not depend on the number of atoms involved.

22
4.1.20 gyration: radius of gyration of a group of atoms.
The block gyration {...} defines the parameters for calculating the radius of gyration of a group of atomic
positions {x1 (t), x2 (t), . . . xN (t)} with respect to their center of geometry, xcog (t):
s
1 N  2
Rgyr = ∑ xi (t) − xcog (t) (7)
N i=1

This component must contain one atoms {...} block to define the atom group, and returns a positive
number, expressed in Å.
List of keywords (see also 4.5 for additional options):
• atoms: see definition of atoms in sec. 4.1.17 (rmsd component)

4.1.21 inertia: total moment of inertia of a group of atoms.

The block inertia {...} defines the parameters for calculating the total moment of inertia of a group of
atomic positions {x1 (t), x2 (t), . . . xN (t)} with respect to their center of geometry, xcog (t):
N  2
I = ∑ xi (t) − xcog (t) (8)
i=1

Note that all atomic masses are set to 1 for simplicity. This component must contain one atoms {...}
block to define the atom group, and returns a positive number, expressed in Å2 .
List of keywords (see also 4.5 for additional options):
• atoms: see definition of atoms in sec. 4.1.17 (rmsd component)

4.1.22 inertiaZ: total moment of inertia of a group of atoms around a chosen axis.
The block inertiaZ {...} defines the parameters for calculating the component along the axis e of the
moment of inertia of a group of atomic positions {x1 (t), x2 (t), . . . xN (t)} with respect to their center of
geometry, xcog (t):
N

2
Ie = ∑ xi (t) − xcog (t) · e (9)
i=1

Note that all atomic masses are set to 1 for simplicity. This component must contain one atoms {...}
block to define the atom group, and returns a positive number, expressed in Å2 .
List of keywords (see also 4.5 for additional options):
• atoms: see definition of atoms in sec. 4.1.17 (rmsd component)

• axis h Projection axis (Å) i

Context: inertiaZ
Acceptable values: (x, y, z) triplet
Default value: (0.0, 0.0, 1.0)
Description: The three components of this vector define (when normalized) the projection axis e.

23
4.1.23 orientation: orientation from reference coordinates.
The block orientation {...} returns the same optimal rotation used in the rmsd component to super-
(ref)
impose the coordinates {xi (t)} onto a set of reference coordinates {xi }. Such component returns a
four dimensional vector q = (q0 , q1 , q2 , q3 ), with ∑i q2i = 1; this quaternion expresses the optimal rota-
(ref)
tion {xi (t)} → {xi } according to the formalism in reference [3]. The quaternion (q0 , q1 , q2 , q3 ) can also
be written as (cos(θ /2), sin(θ /2)u), where θ is the angle and u the normalized axis of rotation; for ex-
ample, a rotation of 90◦ around the z axis is expressed as “(0.707, 0.0, 0.0, 0.707)”. The script
quaternion2rmatrix.tcl provides Tcl functions for converting to and from a 4 × 4 rotation matrix in a
format suitable for usage in VMD.
As for the component rmsd, the available options are atoms, refPositionsFile and refPositions.
Note: refPositionsand refPositionsFile define the set of positions from which the optimal rotation
is calculated, but this rotation is not applied to the coordinates of the atoms involved: it is used instead to
define the variable itself.
List of keywords (see also 4.5 for additional options):
• atoms: see definition of atoms in sec. 4.1.17 (rmsd component)
• refPositions: see definition of refPositions in sec. 4.1.17 (rmsd component)
• refPositionsFile: see definition of refPositionsFile in sec. 4.1.17 (rmsd component)
• closestToQuaternion h Reference rotation i
Context: orientation
Acceptable values: “(q0, q1, q2, q3)” quadruplet
Default value: (1.0, 0.0, 0.0, 0.0) (“null” rotation)
Description: Between the two equivalent quaternions (q0 , q1 , q2 , q3 ) and (−q0 , −q1 , −q2 , −q3 ), the
closer to (1.0, 0.0, 0.0, 0.0) is chosen. This simplifies the visualization of the colvar trajectory
when sampled values are a smaller subset of all possible rotations. Note: this only affects the output,
never the dynamics.
Tip: stopping the rotation of a protein. To stop the rotation of an elongated macromolecule in solution
(and use an anisotropic box to save water molecules), it is possible to define a colvar with an orientation
component, and restrain it throuh the harmonic bias around the identity rotation, (1.0, 0.0, 0.0, 0.0).
Only the overall orientation of the macromolecule is affected, and not its internal degrees of freedom. The
user should also take care that the macromolecule is composed by a single chain, or disable wrapAll other-
wise.

4.1.24 orientationAngle: angle of rotation from reference coordinates.

The block orientationAngle {...} accepts the same base options as the component orientation:
atoms, refPositions, refPositionsFile. The returned value is the angle of rotation θ between the
current and the reference positions. This angle is expressed in degrees within the range [0◦ :180◦ ].
List of keywords (see also 4.5 for additional options):
• atoms: see definition of atoms in sec. 4.1.17 (rmsd component)
• refPositions: see definition of refPositions in sec. 4.1.17 (rmsd component)
• refPositionsFile: see definition of refPositionsFile in sec. 4.1.17 (rmsd component)

24
4.1.25 orientationProj: cosine of the angle of rotation from reference coordinates.
The block orientationProj {...} accepts the same base options as the component orientation: atoms,
refPositions, refPositionsFile. The returned value is the cosine of the angle of rotation θ between the
current and the reference positions. The range of values is [-1:1].
List of keywords (see also 4.5 for additional options):

• atoms: see definition of atoms in sec. 4.1.17 (rmsd component)

• refPositions: see definition of refPositions in sec. 4.1.17 (rmsd component)

• refPositionsFile: see definition of refPositionsFile in sec. 4.1.17 (rmsd component)

4.1.26 spinAngle: angle of rotation around a given axis.

The complete rotation described by orientation can optionally be decomposed into two sub-rotations: one
is a “spin” rotation around e, and the other a “tilt” rotation around an axis orthogonal to e. The component
spinAngle measures the angle of the “spin” sub-rotation around e.
List of keywords (see also 4.5 for additional options):

• atoms: see definition of atoms in sec. 4.1.17 (rmsd component)

• refPositions: see definition of refPositions in sec. 4.1.17 (rmsd component)

• refPositionsFile: see definition of refPositionsFile in sec. 4.1.17 (rmsd component)

• axis h Special rotation axis (Å) i

Context: tilt
Acceptable values: (x, y, z) triplet
Default value: (0.0, 0.0, 1.0)
Description: The three components of this vector define (when normalized) the special rotation axis
used to calculate the tilt and spinAngle components.

The component spinAngle returns an angle (in degrees) within the periodic interval [−180 : 180].
Note: the value of spinAngle is a continuous function almost everywhere, with the exception of con-
figurations with the corresponding “tilt” angle equal to 180◦ (i.e. the tilt component is equal to −1): in
those cases, spinAngle is undefined. If such configurations are expected, consider defining a tilt colvar
using the same axis e, and restraining it with a lower wall away from −1.

4.1.27 tilt: cosine of the rotation orthogonal to a given axis.

The component tilt measures the cosine of the angle of the “tilt” sub-rotation, which combined with the
“spin” sub-rotation provides the complete rotation of a group of atoms. The cosine of the tilt angle rather
than the tilt angle itself is implemented, because the latter is unevenly distributed even for an isotropic
system: consider as an analogy the angle θ in the spherical coordinate system. The component tilt relies
on the same options as spinAngle, including the definition of the axis e. The values of tilt are real
numbers in the interval [−1 : 1]: the value 1 represents an orientation fully parallel to e (tilt angle = 0◦ ), and
the value −1 represents an anti-parallel orientation.
List of keywords (see also 4.5 for additional options):

25
 • atoms: see definition of atoms in sec. 4.1.17 (rmsd component)

• refPositions: see definition of refPositions in sec. 4.1.17 (rmsd component)

• refPositionsFile: see definition of refPositionsFile in sec. 4.1.17 (rmsd component)

• axis: see definition of axis in sec. 4.1.26 (spinAngle component)

4.2 Shared keywords for all components

The following options can be used for any of the above colvar components in order to obtain a polynomial
combination.

• name h Name of this component i

Context: any component
Acceptable values: string
Default value: type of component + numeric id
Description: The name is an unique case-sensitive string which allows the Colvars module to
identify this component. This is useful, for example, when combining multiple components via a
scriptedFunction.

• scalable h Attempt to calculate this component in parallel? i

Context: any component
Acceptable values: boolean
Default value: on, if available
Description: If set to on (default), the Colvars module will attempt to calculate this component
in parallel to reduce overhead. Whether this option is available depends on the type of component:
currently supported are distance, distanceZ, distanceXY, distanceVec, distanceDir, angle and
dihedral. This flag influences computational cost, but does not affect numerical results: therefore, it
should only be turned off for debugging or testing purposes.

4.3 Periodic components

The following components returns real numbers that lie in a periodic interval:

• dihedral: torsional angle between four groups;

• spinAngle: angle of rotation around a predefined axis in the best-fit from a set of reference coordi-
nates.

In certain conditions, distanceZ can also be periodic, namely when periodic boundary conditions (PBCs)
are defined in the simulation and distanceZ’s axis is parallel to a unit cell vector.
In addition, a custom scalar colvar may be periodic depending on its user-defined expression. It will
only be treated as such by the Colvars module if the period is specified using the period keyword, while
wrapAround is optional.
The following keywords can be used within periodic components, or within custom variables (4.6)).

26
 • period h Period of the component i
Context: distanceZ, custom colvars
Acceptable values: positive decimal
Default value: 0.0
Description: Setting this number enables the treatment of distanceZ as a periodic component:
by default, distanceZ is not considered periodic. The keyword is supported, but irrelevant within
dihedral or spinAngle, because their period is always 360 degrees.
• wrapAround h Center of the wrapping interval for periodic variables i
Context: distanceZ, dihedral, spinAngle, custom colvars
Acceptable values: decimal
Default value: 0.0
Description: By default, values of the periodic components are centered around zero, ranging from
−P/2 to P/2, where P is the period. Setting this number centers the interval around this value. This
can be useful for convenience of output, or to set the walls for a harmonicWalls in an order that
would not otherwise be allowed.
Internally, all differences between two values of a periodic colvar follow the minimum image conven-
tion: they are calculated based on the two periodic images that are closest to each other.
Note: linear or polynomial combinations of periodic components (see 4.5) may become meaningless
when components cross the periodic boundary. Use such combinations carefully: estimate the range of
possible values of each component in a given simulation, and make use of wrapAround to limit this problem
whenever possible.

4.4 Non-scalar components

When one of the following components are used, the defined colvar returns a value that is not a scalar
number:
• distanceVec: 3-dimensional vector of the distance between two groups;
• distanceDir: 3-dimensional unit vector of the distance between two groups;
• orientation: 4-dimensional unit quaternion representing the best-fit rotation from a set of reference
coordinates.
The distance between two 3-dimensional unit vectors is computed as the angle between them. The distance
between two quaternions is computed as the angle between the two 4-dimensional unit vectors: because the
orientation represented by q is the same as the one represented by −q, distances between two quaternions
are computed considering the closest of the two symmetric images.
Non-scalar components carry the following restrictions:
• Calculation of total forces (outputTotalForce option) is currently not implemented.
• Each colvar can only contain one non-scalar component.
• Binning on a grid (abf, histogram and metadynamics with useGrids enabled) is currently not im-
plemented for colvars based on such components.
Note: while these restrictions apply to individual colvars based on non-scalar components, no limit is
set to the number of scalar colvars. To compute multi-dimensional histograms and PMFs, use sets of scalar
colvars of arbitrary size.

27
4.4.1 Calculating total forces
In addition to the restrictions due to the type of value computed (scalar or non-scalar), a final restriction
can arise when calculating total force (outputTotalForce option or application of a abf bias). total forces
are available currently only for the following components: distance, distanceZ, distanceXY, angle,
dihedral, rmsd, eigenvector and gyration.

4.5 Linear and polynomial combinations of components

To extend the set of possible definitions of colvars ξ (r), multiple components qi (r) can be summed with the
formula:
ξ (r) = ∑ ci [qi (r)]ni (10)
i

where each component appears with a unique coefficient ci (1.0 by default) the positive integer exponent ni
(1 by default).
Any set of components can be combined within a colvar, provided that they return the same type of
values (scalar, unit vector, vector, or quaternion). By default, the colvar is the sum of its components. Linear
or polynomial combinations (following equation (10)) can be obtained by setting the following parameters,
which are common to all components:

• componentCoeff h Coefficient of this component in the colvar i

Context: any component
Acceptable values: decimal
Default value: 1.0
Description: Defines the coefficient by which this component is multiplied (after being raised to
componentExp) before being added to the sum.

• componentExp h Exponent of this component in the colvar i

Context: any component
Acceptable values: integer
Default value: 1
Description: Defines the power at which the value of this component is raised before being added to
the sum. When this exponent is different than 1 (non-linear sum), total forces and the Jacobian force
are not available, making the colvar unsuitable for ABF calculations.

Example: To define the average of a colvar across different parts of the system, simply define within
the same colvar block a series of components of the same type (applied to different atom groups), and assign
to each component a componentCoeff of 1/N.

4.6 Custom functions

Collective variables may be defined by specifying a custom function as an analytical expression such as
cos(x) + yˆ2. The expression is parsed by the Lepton expression parser (written by Peter Eastman), which
produces efficient evaluation routines for the function itself as well as its derivatives. The expression may
use the collective variable components as variables, refered to as their name string. Scalar elements of vector
components may be accessed by appending a 1-based index to their name. When implementing generic
functions of Cartesian coordinates rather than functions of existing components, the cartesian component

28
may be particularly useful. A scalar-valued custom variable may be manually defined as periodic by pro-
viding the keyword period, and the optional keyword wrapAround, with the same meaning as in periodic
components (see 4.3 for details). A vector variable may be defined by specifying the customFunction pa-
rameter several times: each expression defines one scalar element of the vector colvar. This is illustrated in
the example below.

colvar {
name custom

# A 2-dimensional vector function of a scalar x and a 3-vector r

customFunction cos(x) * (r1 + r2 + r3)
customFunction sqrt(r1 * r2)

distance {
name x
group1 { atomNumbers 1 }
group2 { atomNumbers 50 }
}
distanceVec {
name r
group1 { atomNumbers 10 11 12 }
group2 { atomNumbers 20 21 22 }
}
}

• customFunction h Compute colvar as a custom function of its components i

Context: colvar
Acceptable values: string
Description: Defines the colvar as a scalar expression of its colvar components. Multiple mentions
can be used to define a vector variable (as in the example above).

• customFunctionType h Type of value returned by the scripted colvar i

Context: colvar
Acceptable values: string
Default value: scalar
Description: With this flag, the user may specify whether the colvar is a scalar or one of the following
vector types: vector3 (a 3D vector), unit vector3 (a normalized 3D vector), or unit quaternion
(a normalized quaternion), or vector. Note that the scalar and vector cases are not necessary, as they
are detected automatically.

4.7 Defining grid parameters

Many algorithms require the definition of boundaries and/or characteristic spacings that can be used to
define discrete “states” in the collective variable, or to combine variables with very different units. The
parameters described below offer a way to specify these parameters only once for each variable, while using
them multiple times in restraints, time-dependent biases or analysis methods.

29
• width h Unit of the variable, or grid spacing i
Context: colvar
Acceptable values: positive decimal
Default value: 1.0
Description: This number defines the effective unit of measurement for the collective variable, and
is used by the biasing methods for the following purposes. Harmonic (6.4), harmonic walls (6.6)
and linear restraints (6.7) use it to set the physical unit of the force constant, which is useful for
multidimensional restraints involving multiple variables with very different units (for examples, Å or
degrees ◦ ) with a single, scaled force constant. The values of the scaled force constant in the units of
each variable are printed at initialization time. Histograms (6.9), ABF (6.1) and metadynamics (6.3)
all use this number as the initial choice for the grid spacing along this variable: for this reason, width
should generally be no larger than the standard deviation of the colvar in an unbiased simulation.
Unless it is required to control the spacing, it is usually simplest to keep the default value of 1, so that
restraint force constants are provided with their full physical unit.
• lowerBoundary h Lower boundary of the colvar i
Context: colvar
Acceptable values: decimal
Description: Defines the lowest end of the interval of “relevant” values for the colvar. This number
can be either a true physical boundary, or a user-defined number. Together with upperBoundary and
width, it is used to define a grid of values along the variable (not available for variables with vector
values, 4.4). This option does not affect dynamics: to confine a colvar within a certain interval, use a
harmonicWalls bias.
• upperBoundary h Upper boundary of the colvar i
Context: colvar
Acceptable values: decimal
Description: Similarly to lowerBoundary, defines the highest possible or allowed value.
• hardLowerBoundary h Whether the lower boundary is the physical lower limit i
Context: colvar
Acceptable values: boolean
Default value: off
Description: This option does not affect simulation results, but enables some internal optimizations.
Depending on its mathematical definition, a colvar may have “natural” boundaries: for example, a
distance colvar has a “natural” lower boundary at 0. Setting this option instructs the Colvars module
that the user-defined lower boundary is “natural”. See Section 4.1 for the physical ranges of values of
each component.
• hardUpperBoundary h Whether the upper boundary is the physical upper limit of the colvar’s
values i
Context: colvar
Acceptable values: boolean
Default value: off
Description: Analogous to hardLowerBoundary.
• expandBoundaries h Allow to expand the two boundaries if needed i
Context: colvar
Acceptable values: boolean
Default value: off

30
 Description: If defined, biasing and analysis methods may keep their own copies of lowerBoundary
and upperBoundary, and expand them to accommodate values that do not fit in the initial range.
Currently, this option is used by the metadynamics bias (6.3) to keep all of its hills fully within the
grid. This option cannot be used when the initial boundaries already span the full period of a periodic
colvar.

4.8 Trajectory output

• outputValue h Output a trajectory for this colvar i
Context: colvar
Acceptable values: boolean
Default value: on
Description: If colvarsTrajFrequency is non-zero, the value of this colvar is written to the trajec-
tory file every colvarsTrajFrequency steps in the column labeled “<name>”.

• outputVelocity h Output a velocity trajectory for this colvar i

Context: colvar
Acceptable values: boolean
Default value: off
Description: If colvarsTrajFrequency is defined, the finite-difference calculated velocity of this
colvar are written to the trajectory file under the label “v <name>”.

• outputEnergy h Output an energy trajectory for this colvar i

Context: colvar
Acceptable values: boolean
Default value: off
Description: This option applies only to extended Lagrangian colvars. If colvarsTrajFrequency is
defined, the kinetic energy of the extended degree and freedom and the potential energy of the restrain-
ing spring are are written to the trajectory file under the labels “Ek <name>” and “Ep <name>”.

• outputTotalForce h Output a total force trajectory for this colvar i

Context: colvar
Acceptable values: boolean
Default value: off
Description: If colvarsTrajFrequency is defined, the total force on this colvar (i.e. the projection
of all atomic total forces onto this colvar — see equation (15) in section 6.1) are written to the trajec-
tory file under the label “fs <name>”. For extended Lagrangian colvars, the “total force” felt by the
extended degree of freedom is simply the force from the harmonic spring. Note: not all components
support this option. The physical unit for this force is the unit of energy specified by units, divided
by the colvar unit U.

• outputAppliedForce h Output an applied force trajectory for this colvar i

Context: colvar
Acceptable values: boolean
Default value: off
Description: If colvarsTrajFrequency is defined, the total force applied on this colvar by Colvars
biases are written to the trajectory under the label “fa <name>”. For extended Lagrangian colvars,

31
 this force is actually applied to the extended degree of freedom rather than the geometric colvar itself.
The physical unit for this force is the unit of energy specified by units divided by the colvar unit.

4.9 Extended Lagrangian

The following options enable extended-system dynamics, where a colvar is coupled to an additional degree
of freedom (fictitious particle) by a harmonic spring. All biasing and confining forces are then applied to the
extended degree of freedom. The “actual” geometric colvar (function of Cartesian coordinates) only feels
the force from the harmonic spring. This is particularly useful when combined with an ABF bias (6.1) to
perform eABF simulations (6.2).

• extendedLagrangian h Add extended degree of freedom i

Context: colvar
Acceptable values: boolean
Default value: off
Description: Adds a fictitious particle to be coupled to the colvar by a harmonic spring. The
fictitious mass and the force constant of the coupling potential are derived from the parameters
extendedTimeConstant and extendedFluctuation, described below. Biasing forces on the colvar
are applied to this fictitious particle, rather than to the atoms directly. This implements the extended
Lagrangian formalism used in some metadynamics simulations [2].

• extendedFluctuation h Standard deviation between the colvar and the fictitious particle (colvar
unit) i
Context: colvar
Acceptable values: positive decimal
Description: Defines the spring stiffness for the extendedLagrangian mode, by setting the typi-
cal deviation between the colvar and the extended degree of freedom due to thermal fluctuation. The
spring force constant is calculated internally as kB T /σ 2 , where σ is the value of extendedFluctuation.

• extendedTimeConstant h Oscillation period of the fictitious particle (fs) i

Context: colvar
Acceptable values: positive decimal
Default value: 200
Description: Defines the inertial mass of the fictitious particle, by setting the oscillation period of the
harmonic oscillator formed by the fictitious particle and the spring. The period should be much larger
than the MD time step to ensure accurate integration of the extended particle’s equation of motion.
The fictitious mass is calculated internally as kB T (τ/2πσ )2 , where τ is the period and σ is the typical
fluctuation (see above).

• extendedTemp h Temperature for the extended degree of freedom (K) i

Context: colvar
Acceptable values: positive decimal
Default value: thermostat temperature
Description: Temperature used for calculating the coupling force constant of the extended variable
(see extendedFluctuation) and, if needed, as a target temperature for extended Langevin dynamics
(see extendedLangevinDamping). This should normally be left at its default value.

32
 • extendedLangevinDamping h Damping factor for extended Langevin dynamics (ps−1 ) i
Context: colvar
Acceptable values: positive decimal
Default value: 1.0
Description: If this is non-zero, the extended degree of freedom undergoes Langevin dynamics
at temperature extendedTemp. The friction force is minus extendedLangevinDamping times the
velocity. This is useful because the extended dynamics coordinate may heat up in the transient non-
equilibrium regime of ABF. Use moderate damping values, to limit viscous friction (potentially slow-
ing down diffusive sampling) and stochastic noise (increasing the variance of statistical measure-
ments). In doubt, use the default value.

4.10 Backward-compatibility
• subtractAppliedForce h Do not include biasing forces in the total force for this colvar i
Context: colvar
Acceptable values: boolean
Default value: off
Description: If the colvar supports total force calculation (see 4.4.1), all forces applied to this
colvar by biases will be removed from the total force. This keyword allows to recover some of the
“system force” calculation available in the Colvars module before version 2016-08-10. Please note
that removal of all other external forces (including biasing forces applied to a different colvar) is
no longer supported, due to changes in the underlying simulation engines (primarily NAMD). This
option may be useful when continuing a previous simulation where the removal of external/applied
forces is essential. For all new simulations, the use of this option is not recommended.

4.11 Statistical analysis

Run-time calculations of statistical properties that depend explicitly on time can be performed for individual
collective variables. Currently, several types of time correlation functions, running averages and running
standard deviations are implemented. For run-time computation of histograms, please see the histogram
bias (6.9).

• corrFunc h Calculate a time correlation function? i

Context: colvar
Acceptable values: boolean
Default value: off
Description: Whether or not a time correlaction function should be calculated for this colvar.

• corrFuncWithColvar h Colvar name for the correlation function i

Context: colvar
Acceptable values: string
Description: By default, the auto-correlation function (ACF) of this colvar, ξi , is calculated. When
this option is specified, the correlation function is calculated instead with another colvar, ξ j , which
must be of the same type (scalar, vector, or quaternion) as ξi .

33
• corrFuncType h Type of the correlation function i
Context: colvar
Acceptable values: velocity, coordinate or coordinate p2
Default value: velocity

Description: With coordinate or velocity, the correlation function Ci, j (t) = Π (ξi (t0 ), ξ j (t0 + t))
is calculated between the variables ξi and ξ j , or their velocities. Π(ξi , ξ j ) is the scalar product
when calculated between scalar or vector values, whereas for quaternions it is the cosine between
the two corresponding rotation axes. With coordinate p2, the second order Legendre polynomial,
(3 cos(θ )2 − 1)/2, is used instead of the cosine.
• corrFuncNormalize h Normalize the time correlation function? i
Context: colvar
Acceptable values: boolean
Default value: on
Description:
If enabled,  the value of the correlation function at t = 0 is normalized to 1; otherwise,
it equals to O (ξi , ξ j ) .
• corrFuncLength h Length of the time correlation function i
Context: colvar
Acceptable values: positive integer
Default value: 1000
Description: Length (in number of points) of the time correlation function.
• corrFuncStride h Stride of the time correlation function i
Context: colvar
Acceptable values: positive integer
Default value: 1
Description: Number of steps between two values of the time correlation function.
• corrFuncOffset h Offset of the time correlation function i
Context: colvar
Acceptable values: positive integer
Default value: 0
Description: The starting time (in number of steps) of the time correlation function (default: t = 0).
Note: the value at t = 0 is always used for the normalization.
• corrFuncOutputFile h Output file for the time correlation function i
Context: colvar
Acceptable values: UNIX filename
Default value: output.<name>.corrfunc.dat
Description: The time correlation function is saved in this file.
• runAve h Calculate the running average and standard deviation i
Context: colvar
Acceptable values: boolean
Default value: off
Description: Whether or not the running average and standard deviation should be calculated for
this colvar.
• runAveLength h Length of the running average window i
Context: colvar

34
 Acceptable values: positive integer
Default value: 1000
Description: Length (in number of points) of the running average window.

• runAveStride h Stride of the running average window values i

Context: colvar
Acceptable values: positive integer
Default value: 1
Description: Number of steps between two values within the running average window.

• runAveOutputFile h Output file for the running average and standard deviation i
Context: colvar
Acceptable values: UNIX filename
Default value: output.<name>.runave.traj
Description: The running average and standard deviation are saved in this file.

35
5 Selecting atoms
To define collective variables, atoms are usually selected as groups. Each group is defined using an iden-
tifier that is unique in the context of the specific colvar component (e.g. for a distance component, the two
groups are group1 and group2). The identifier is followed by a brace-delimited block containing selection
keywords and other parameters, including an optional name:

• name h Unique name for the atom group i

Context: atom group
Acceptable values: string
Description: This parameter defines a unique name for this atom group, which can be referred to
in the definition of other atom groups (including in other colvars) by invoking atomsOfGroup as a
selection keyword.

5.1 Atom selection keywords

Selection keywords may be used individually or in combination with each other, and each can be repeated
any number of times. Selection is incremental: each keyword adds the corresponding atoms to the selection,
so that different sets of atoms can be combined. However, atoms included by multiple keywords are only
counted once. Below is an example configuration for an atom group called “atoms”. Note: this is an un-
usually varied combination of selection keywords, demonstrating how they can be combined together: most
simulations only use one of them.

atoms {

# add atoms 1 and 3 to this group (note: the first atom in the system is 1)
atomNumbers {
1 3
}

# add atoms starting from 20 up to and including 50

atomNumbersRange 20-50

# add index group (requires a .ndx file to be provided globally)

indexGroup Water
}

The resulting selection includes atoms 1 and 3, those between 20 and 50, and those in the index group
called “Water”. The indices of this group are read from the file provided by the global keyword indexFile.
The complete list of selection keywords available in LAMMPS is:

• atomNumbers h List of atom numbers i

Context: atom group
Acceptable values: space-separated list of positive integers

36
 Description: This option adds to the group all the atoms whose numbers are in the list. The number
of the first atom in the system is 1: to convert from a VMD selection, use “atomselect get serial”.

• indexGroup h Name of index group to be used (GROMACS format) i

Context: atom group
Acceptable values: string
Description: If the name of an index file has been provided by indexFile, this option allows to
select one index group from that file: the atoms from that index group will be used to define the
current group.

• atomsOfGroup h Name of group defined previously i

Context: atom group
Acceptable values: string
Description: Refers to a group defined previously using its user-defined name. This adds all atoms
of that named group to the current group.

• atomNumbersRange h Atoms within a number range i

Context: atom group
Acceptable values: <Starting number>-<Ending number>
Description: This option includes in the group all atoms whose numbers are within the range speci-
fied. The number of the first atom in the system is 1.

• dummyAtom h Dummy atom position (Å) i

Context: atom group
Acceptable values: (x, y, z) triplet
Description: Instead of selecting any atom, this option makes the group a virtual particle at a fixed
position in space. This is useful e.g. to replace a group’s center of geometry with a user-defined
position.

5.2 Moving frame of reference.

The following options define an automatic calculation of an optimal translation (centerReference) or
optimal rotation (rotateReference), that superimposes the positions of this group to a provided set of
reference coordinates. This can allow, for example, to effectively remove from certain colvars the effects of
molecular tumbling and of diffusion. Given the set of atomic positions xi , the colvar ξ can be defined on a
set of roto-translated positions x0i = R(xi − xC ) + xref . xC is the geometric center of the xi , R is the optimal
rotation matrix to the reference positions and xref is the geometric center of the reference positions.
Components that are defined based on pairwise distances are naturally invariant under global roto-
translations. Other components are instead affected by global rotations or translations: however, they can
be made invariant if they are expressed in the frame of reference of a chosen group of atoms, using the
centerReference and rotateReference options. Finally, a few components are defined by convention
using a roto-translated frame (e.g. the minimal RMSD): for these components, centerReference and
rotateReference are enabled by default. In typical applications, the default settings result in the expected
behavior.

Warning on rotating frames of reference and periodic boundary conditions. rotateReference af-
fects coordinates that depend on minimum-image distances in periodic boundary conditions (PBC). After

37
rotation of the coordinates, the periodic cell vectors become irrelevant: the rotated system is effectively
non-periodic. A safe way to handle this is to ensure that the relevant inter-group distance vectors remain
smaller than the half-size of the periodic cell. If this is not desirable, one should avoid the rotating frame of
reference, and apply orientational restraints to the reference group instead, in order to keep the orientation
of the reference group consistent with the orientation of the periodic cell.

Warning on rotating frames of reference and ABF. Note that centerReference and rotateReference
may affect the Jacobian derivative of colvar components in a way that is not taken into account by default.
Be careful when using these options in ABF simulations or when using total force values.

• centerReference h Implicitly remove translations for this group i

Context: atom group
Acceptable values: boolean
Default value: off
Description: If this option is on, the center of geometry of the group will be aligned with that of
the reference positions provided by refPositions or refPositionsFile. Colvar components will
only have access to the aligned positions. Note: unless otherwise specified, rmsd and eigenvector
set this option to on by default.

• rotateReference h Implicitly remove rotations for this group i

Context: atom group
Acceptable values: boolean
Default value: off
Description: If this option is on, the coordinates of this group will be optimally superimposed
to the reference positions provided by refPositions or refPositionsFile. The rotation will be
performed around the center of geometry if centerReference is on, or around the origin otherwise.
The algorithm used is the same employed by the orientation colvar component [3]. Forces applied
to the atoms of this group will also be implicitly rotated back to the original frame. Note: unless
otherwise specified, rmsd and eigenvector set this option to on by default.

• refPositions h Reference positions for fitting (Å) i

Context: atom group
Acceptable values: space-separated list of (x, y, z) triplets
Description: This option provides a list of reference coordinates for centerReference and/or
rotateReference, and is mutually exclusive with refPositionsFile. If only centerReference
is on, the list may contain a single (x, y, z) triplet; if also rotateReference is on, the list should be
as long as the atom group, and its order must match the order in which atoms were defined.

• refPositionsFile h File containing the reference positions for fitting i

Context: atom group
Acceptable values: UNIX filename
Description: This option provides a list of reference coordinates for centerReference and/or
rotateReference, and is mutually exclusive with refPositions. The acceptable file format is XYZ,
which is read in double precision. Atomic positions are read differently depending on the following
scenarios: (i) the file contains exactly as many records as the atoms in the group: all positions are
read in sequence; (ii) (most common case) the file contains coordinates for the entire system: only the
positions corresponding to the numeric indices of the atom group are read. In each case, atoms are
read from the file in order of increasing number.

38
 • fittingGroup h Use an alternate set of atoms to define the roto-translation i
Context: atom group
Acceptable values: Block fittingGroup { ... }
Default value: This group itself
Description: If either centerReference or rotateReference is defined, this keyword defines an
alternate atom group to calculate the optimal roto-translation. Use this option to define a continuous
rotation if the structure of the group involved changes significantly (a typical symptom would be the
message “Warning: discontinuous rotation!”).
# Example: defining a group "atoms", with its coordinates expressed
# on a roto-translated frame of reference defined by a second group
atoms {

psfSegID PROT
atomNameResidueRange CA 41-48

centerReference yes
rotateReference yes
fittingGroup {
# define the frame by fitting the rest of the protein
psfSegID PROT PROT
atomNameResidueRange CA 1-40
atomNameResidueRange CA 49-100
}
refPositionsFile all.pdb # can be the entire system
}

The following two options have default values appropriate for the vast majority of applications, and are
only provided to support rare, special cases.

• enableFitGradients h Include the roto-translational contribution to colvar gradients i

Context: atom group
Acceptable values: boolean
Default value: on
Description: When either centerReference or rotateReference is on, the gradients of some
colvars include terms proportional to ∂ R/∂ xi (rotational gradients) and ∂ xC /∂ xi (translational gradi-
ents). By default, these terms are calculated and included in the total gradients; if this option is set
to off, they are neglected. In the case of a minimum RMSD component, this flag is automatically
disabled because the contributions of those derivatives to the gradients cancel out.

• enableForces h Apply forces from this colvar to this group i

Context: atom group
Acceptable values: boolean
Default value: on
Description: If this option is off, no forces are applied the atoms in the group. Other forces are not
affected (i.e. those from the MD engine, from other colvars, and other external forces). For dummy
atoms, this option is off by default.

39
5.3 Treatment of periodic boundary conditions.
In simulations with periodic boundary conditions, many of the implemented colvar components rely on the
fact that each position within a group of atoms is at the nearest periodic image from the center of geometry
of the group itself. However, due to the internal wrapping of individual atomic positions done by LAMMPS,
this assumption is broken if the group straddles one of the unit cell’s boundaries. For this reason, within the
Colvars module all coordinates are unwrapped by default to avoid discontinuities (see unwrap keyword in
3.1).
The user should determine whether maintaining the default value of unwrap, depending on the specifics
of each system. In general, internal coordinate wrapping by LAMMPS does not affect the calculation of
colvars if each atom group satisfies one or more of the following:

i) it is composed by only one atom;

ii) it is used by a colvar component which does not make use of its center of geometry, but only of
pairwise distances (distanceInv, coordNum, hBond, alpha, dihedralPC);

iii) it is used by a colvar component that ignores the ill-defined Cartesian components of its center of
mass (such as the x and y components of a membrane’s center of mass modeled with distanceZ).

5.4 Performance of a Colvars calculation based on group size.

In simulations performed with message-passing programs (such as NAMD or LAMMPS), the calculation of
energy and forces is distributed (i.e., parallelized) across multiple nodes, as well as over the processor cores
of each node. When Colvars is enabled, certain atomic coordinates are collected on a single node, where
the calculation of collective variables and of their biases is executed. This means that for simulations over
large numbers of nodes, a Colvars calculation may produce a significant overhead, coming from the costs of
transmitting atomic coordinates to one node and of processing them.
Performance can be improved in multiple ways:

• The calculation of variables, components and biases can be distributed over the processor cores of the
node where the Colvars module is executed. Currently, an equal weight is assigned to each colvar,
or to each component of those colvars that include more than one component. The performance of
simulations that use many colvars or components is improved automatically. For simulations that use
a single large colvar, it may be advisable to partition it in multiple components, which will be then
distributed across the available cores. In LAMMPS, this feature is supported automatically when
LAMMPS is compiled with OpenMP support. If printed, the message “SMP parallelism is available.”
indicates the availability of the option. If available, the option is turned on by default, but may be
disabled using the keyword smp if required for debugging.

• As a general rule, the size of atom groups should be kept relatively small (up to a few thousands
of atoms, depending on the size of the entire system in comparison). To gain an estimate of the
computational cost of a large colvar, one can use a test calculation of the same colvar in VMD (hint:
use the time Tcl command to measure the cost of running cv update).

40
6 Biasing and analysis methods
All of the biasing and analysis methods implemented recognize the following options:

• name h Identifier for the bias i

Context: colvar bias
Acceptable values: string
Default value: <type of bias><bias index>
Description: This string is used to identify the bias or analysis method in output messages and to
name some output files.

• colvars h Collective variables involved i

Context: colvar bias
Acceptable values: space-separated list of colvar names
Description: This option selects by name all the colvars to which this bias or analysis will be applied.

• outputEnergy h Write the current bias energy to the trajectory file i

Context: colvar bias
Acceptable values: boolean
Default value: off
Description: If this option is chosen and colvarsTrajFrequency is not zero, the current value of
the biasing energy will be written to the trajectory file during the simulation.

In addition, restraint biases (6.4, 6.6, 6.7, ...) and metadynamics biases (6.3) offer the following optional
keywords, which allow the use of thermodynamic integration (TI) to compute potentials of mean force
(PMFs). In adaptive biasing force (ABF) biases (6.1) the same keywords are not recognized because their
functionality is always included.

• writeTIPMF h Write the PMF computed by thermodynamic integration i

Context: colvar bias
Acceptable values: boolean
Default value: off
Description: If the bias is applied to a variable that supports the calculation of total forces (see
outputTotalForce and 4.4.1), this option allows calculating the corresponding PMF by thermody-
nanic integration, and writing it to the file output.<name>.ti.pmf, where <name> is the name of
the bias. The total force includes the forces applied to the variable by all bias, except those from this
bias itself. If any bias applies time-dependent forces besides the one using this option, an error is
raised.

• writeTISamples h Write the free-energy gradient samples i

Context: colvar bias
Acceptable values: boolean
Default value: off
Description: This option allows to compute total forces for use with thermodynamic integration
as done by the keyword writeTIPMF. The names of the files containing the variables’ histogram
and mean thermodyunamic forces are output.<name>.ti.count and output.<name>.ti.grad, re-
spectively: these can be used by abf integrate or similar utility. This option on by default when

41
 writeTIPMF is on, but can be enabled separately if the bias is applied to more than one variable,
making not possible the direct integration of the PMF at runtime. If any bias applies time-dependent
forces besides the one using this option, an error is raised.

6.1 Adaptive Biasing Force

For a full description of the Adaptive Biasing Force method, see reference [4]. For details about this im-
plementation, see references [5] and [6]. When publishing research that makes use of this functionality,
please cite references [4] and [6].
An alternate usage of this feature is the application of custom tabulated biasing potentials to one or more
colvars. See inputPrefix and updateBias below.
Combining ABF with the extended Lagrangian feature (4.9) of the variables produces the extended-
system ABF variant of the method (6.2).
ABF is based on the thermodynamic integration (TI) scheme for computing free energy profiles. The free
energy as a function of a set of collective variables ξ = (ξi )i∈[1,n] is defined from the canonical distribution
of ξ , P(ξ ):

1
A(ξ ) = − ln P(ξ ) + A0 (11)
β
In the TI formalism, the free energy is obtained from its gradient, which is generally calculated in the
form of the average of a force F ξ exerted on ξ , taken over an iso-ξ surface:


∇ξ A(ξ ) = −F ξ ξ (12)

Several formulae that take the form of (12) have been proposed. This implementation relies partly on
the classic formulation [7], and partly on a more versatile scheme originating in a work by Ruiz-Montero
et al. [8], generalized by den Otter [9] and extended to multiple variables by Ciccotti et al. [10]. Consider
a system subject to constraints of the form σk (x) = 0. Let (vi )i∈[1,n] be arbitrarily chosen vector fields
(R3N → R3N ) verifying, for all i, j, and k:

vi · ∇x ξ j = δi j (13)
vi · ∇x σk = 0 (14)

then the following holds [10]:

∂A
= hvi · ∇x V − kB T ∇x · vi iξ (15)
∂ ξi
where V is the potential energy function. vi can be interpreted as the direction along which the force
acting on variable ξi is measured, whereas the second term in the average corresponds to the geometric
entropy contribution that appears as a Jacobian correction in the classic formalism [7]. Condition (13) states
that the direction along which the total force on ξi is measured is orthogonal to the gradient of ξ j , which
means that the force measured on ξi does not act on ξ j .
Equation (14) implies that constraint forces are orthogonal to the directions along which the free en-
ergy gradient is measured, so that the measurement is effectively performed on unconstrained degrees of
freedom.

42
 In the framework of ABF, Fξ is accumulated in bins of finite size δ ξ , thereby providing an estimate of
the free energy gradient according to equation (12). The biasing force applied along the collective variables
to overcome free energy barriers is calculated as:

FABF = α(Nξ ) × ∇x A(ξ

e ) (16)

where ∇x Ae denotes the current estimate of the free energy gradient at the current point ξ in the collective
variable subspace, and α(Nξ ) is a scaling factor that is ramped from 0 to 1 as the local number of samples Nξ
increases to prevent nonequilibrium effects in the early phase of the simulation, when the gradient estimate
has a large variance. See the fullSamples parameter below for details.
As sampling of the phase space proceeds, the estimate ∇x A e is progressively refined. The biasing force
introduced in the equations of motion guarantees that in the bin centered around ξ , the forces acting along
the selected collective variables average to zero over time. Eventually, as the undelying free energy surface
is canceled by the adaptive bias, evolution of the system along ξ is governed mainly by diffusion. Although
this implementation of ABF can in principle be used in arbitrary dimension, a higher-dimension collective
variable space is likely to result in sampling difficulties. Most commonly, the number of variables is one or
two.

6.1.1 ABF requirements on collective variables

The following conditions must be met for an ABF simulation to be possible and to produce an accurate
estimate of the free energy profile. Note that these requirements do not apply when using the extended-
system ABF method (6.2).

1. Only linear combinations of colvar components can be used in ABF calculations.

2. Availability of total forces is necessary. The following colvar components can be used in ABF calcu-
lations: distance, distance xy, distance z, angle, dihedral, gyration, rmsd and eigenvector.
Atom groups may not be replaced by dummy atoms, unless they are excluded from the force mea-
surement by specifying oneSiteTotalForce, if available.

3. Mutual orthogonality of colvars. In a multidimensional ABF calculation, equation (13) must be satis-
fied for any two colvars ξi and ξ j . Various cases fulfill this orthogonality condition:

• ξi and ξ j are based on non-overlapping sets of atoms.

• atoms involved in the force measurement on ξi do not participate in the definition of ξ j . This
can be obtained using the option oneSiteTotalForce of the distance, angle, and dihedral
components (example: Ramachandran angles φ , ψ).
• ξi and ξ j are orthogonal by construction. Useful cases are the sum and difference of two com-
ponents, or distance z and distance xy using the same axis.

4. Mutual orthogonality of components: when several components are combined into a colvar, it is
assumed that their vectors vi (equation (15)) are mutually orthogonal. The cases described for colvars
in the previous paragraph apply.

5. Orthogonality of colvars and constraints: equation 14 can be satisfied in two simple ways, if either no
constrained atoms are involved in the force measurement (see point 3 above) or pairs of atoms joined
by a constrained bond are part of an atom group which only intervenes through its center (center of
mass or geometric center) in the force measurement. In the latter case, the contributions of the two

43
 atoms to the left-hand side of equation 14 cancel out. For example, all atoms of a rigid TIP3P water
molecule can safely be included in an atom group used in a distance component.

6.1.2 Parameters for ABF

ABF depends on parameters from collective variables to define the grid on which free energy gradients are
computed. In the direction of each colvar, the grid ranges from lowerBoundary to upperBoundary, and the
bin width (grid spacing) is set by the width parameter. The following specific parameters can be set in the
ABF configuration block:

• name: see definition of name in sec. 6 (biasing and analysis methods)

• colvars: see definition of colvars in sec. 6 (biasing and analysis methods)

• fullSamples h Number of samples in a bin prior to application of the ABF i

Context: abf
Acceptable values: positive integer
Default value: 200
Description: To avoid nonequilibrium effects due to large fluctuations of the force exerted along the
colvars, it is recommended to apply a biasing force only after a the estimate has started converging.
If fullSamples is non-zero, the applied biasing force is scaled by a factor α(Nξ ) between 0 and 1. If
the number of samples Nξ in the current bin is higher than fullSamples, the factor is one. If it is less
than half of fullSamples, the factor is zero and no bias is applied. Between those two thresholds, the
factor follows a linear ramp from 0 to 1: α(Nξ ) = (2Nξ /fullSamples) − 1 .

• maxForce h Maximum magnitude of the ABF force i

Context: abf
Acceptable values: positive decimals (one per colvar)
Default value: disabled
Description: This option enforces a cap on the magnitude of the biasing force effectively applied by
this ABF bias on each colvar. This can be useful in the presence of singularities in the PMF such as
hard walls, where the discretization of the average force becomes very inaccurate, causing the colvar’s
diffusion to get “stuck” at the singularity. To enable this cap, provide one non-negative value for each
colvar. The unit of force is the unit of energy specified by units divided by the colvar unit.

• hideJacobian h Remove geometric entropy term from calculated free energy gradient? i
Context: abf
Acceptable values: boolean
Default value: no
Description: In a few special cases, most notably distance-based variables, an alternate definition
of the potential of mean force is traditionally used, which excludes the Jacobian term describing the
effect of geometric entropy on the distribution of the variable. This results, for example, in particle-
particle potentials of mean force being flat at large separations. Setting this parameter to yes causes
the output data to follow that convention, by removing this contribution from the output gradients
while applying internally the corresponding correction to ensure uniform sampling. It is not allowed
for colvars with multiple components.

44
• outputFreq h Frequency (in timesteps) at which ABF data files are refreshed i
Context: abf
Acceptable values: positive integer
Default value: Colvars module restart frequency
Description: The files containing the free energy gradient estimate and sampling histogram (and the
PMF in one-dimensional calculations) are written on disk at the given time interval.

• historyFreq h Frequency (in timesteps) at which ABF history files are accumulated i
Context: abf
Acceptable values: positive integer
Default value: 0
Description: If this number is non-zero, the free energy gradient estimate and sampling histogram
(and the PMF in one-dimensional calculations) are appended to files on disk at the given time interval.
History file names use the same prefix as output files, with “.hist” appended.

• inputPrefix h Filename prefix for reading ABF data i

Context: abf
Acceptable values: list of strings
Description: If this parameter is set, for each item in the list, ABF tries to read a gradient and a
sampling files named <inputPrefix>.grad and <inputPrefix>.count. This is done at startup
and sets the initial state of the ABF algorithm. The data from all provided files is combined appropri-
ately. Also, the grid definition (min and max values, width) need not be the same that for the current
run. This command is useful to piece together data from simulations in different regions of collective
variable space, or change the colvar boundary values and widths. Note that it is not recommended
to use it to switch to a smaller width, as that will leave some bins empty in the finer data grid. This
option is NOT compatible with reading the data from a restart file (input keyword of the fix ID
group-ID colvars command).

• applyBias h Apply the ABF bias? i

Context: abf
Acceptable values: boolean
Default value: yes
Description: If this is set to no, the calculation proceeds normally but the adaptive biasing force is
not applied. Data is still collected to compute the free energy gradient. This is mostly intended for
testing purposes, and should not be used in routine simulations.

• updateBias h Update the ABF bias? i

Context: abf
Acceptable values: boolean
Default value: yes
Description: If this is set to no, the initial biasing force (e.g. read from a restart file or through
inputPrefix) is not updated during the simulation. As a result, a constant bias is applied. This can
be used to apply a custom, tabulated biasing potential to any combination of colvars. To that effect,
one should prepare a gradient file containing the gradient of the potential to be applied (negative of
the bias force), and a count file containing only values greater than fullSamples. These files must
match the grid parameters of the colvars.

45
6.1.3 Output files
The ABF bias produces the following files, all in multicolumn text format:

• output.grad: current estimate of the free energy gradient (grid), in multicolumn;

• output.count: histogram of samples collected, on the same grid;

• output.pmf: only for one-dimensional calculations, integrated free energy profile or PMF.

If several ABF biases are defined concurrently, their name is inserted to produce unique filenames for
output, as in output.abf1.grad. This should not be done routinely and could lead to meaningless results:
only do it if you know what you are doing!
If the colvar space has been partitioned into sections (windows) in which independent ABF simulations
have been run, the resulting data can be merged using the inputPrefix option described above (a run of 0
steps is enough).

6.1.4 Post-processing: reconstructing a multidimensional free energy surface

If a one-dimensional calculation is performed, the estimated free energy gradient is automatically integrated
and a potential of mean force is written under the file name <outputName>.pmf, in a plain text format that
can be read by most data plotting and analysis programs (e.g. gnuplot).
In dimension 2 or greater, integrating the discretized gradient becomes non-trivial. The standalone
utility abf integrate is provided to perform that task. abf integrate reads the gradient data and uses
it to perform a Monte-Carlo (M-C) simulation in discretized collective variable space (specifically, on the
same grid used by ABF to discretize the free energy gradient). By default, a history-dependent bias (similar
in spirit to metadynamics) is used: at each M-C step, the bias at the current position is incremented by a
preset amount (the hill height). Upon convergence, this bias counteracts optimally the underlying gradient;
it is negated to obtain the estimate of the free energy surface.
abf integrate is invoked using the command-line:
abf integrate <gradient file> [-n <nsteps>] [-t <temp>] [-m (0|1)] [-h <hill height>] [-f
<factor>]
The gradient file name is provided first, followed by other parameters in any order. They are described
below, with their default value in square brackets:

• -n: number of M-C steps to be performed; by default, a minimal number of steps is chosen based on
the size of the grid, and the integration runs until a convergence criterion is satisfied (based on the
RMSD between the target gradient and the real PMF gradient)
• -t: temperature for M-C sampling (unrelated to the simulation temperature) [500 K]
• -m: use metadynamics-like biased sampling? (0 = false) [1]
• -h: increment for the history-dependent bias (“hill height”) [0.01 kcal/mol]
• -f: if non-zero, this factor is used to scale the increment stepwise in the second half of the M-C
sampling to refine the free energy estimate [0.5]

Using the default values of all parameters should give reasonable results in most cases.

abf integrate produces the following output files:

• <gradient file>.pmf: computed free energy surface

46
 • <gradient file>.histo: histogram of M-C sampling (not usable in a straightforward way if the
history-dependent bias has been applied)
• <gradient file>.est: estimated gradient of the calculated free energy surface (from finite differ-
ences)
• <gradient file>.dev: deviation between the user-provided numerical gradient and the actual gradi-
ent of the calculated free energy surface. The RMS norm of this vector field is used as a convergence
criteria and displayed periodically during the integration.
Note: Typically, the “deviation” vector field does not vanish as the integration converges. This happens
because the numerical estimate of the gradient does not exactly derive from a potential, due to numerical
approximations used to obtain it (finite sampling and discretization on a grid).

6.2 Extended-system Adaptive Biasing Force (eABF)

Extended-system ABF (eABF) is a variant of ABF (6.1) where the bias is not applied directly to the col-
lective variable, but to an extended coordinate (“fictitious variable”) λ that evolves dynamically according
to Newtonian or Langevin dynamics. Such an extended coordinate is enabled for a given colvar using the
extendedLagrangian and associated keywords (4.9). The theory of eABF and the present implementation
are documented in detail in reference [11].
Defining an ABF bias on a colvar wherein the extendedLagrangian option is active will perform eABF;
there is no dedicated option.
The extended variable λ is coupled to the colvar z = ξ (q) by the harmonic potential (k/2)(z − λ )2 .
Under eABF dynamics, the adaptive bias on λ is the running estimate of the average spring force:
F bias (λ ∗ ) = hk(λ − z)iλ ∗ (17)
where the angle brackets indicate a canonical average conditioned by λ = λ ∗ . At long simulation times,
eABF produces a flat histogram of the extended variable λ , and a flattened histogram of ξ , whose exact
shape depends on the strength of the coupling as defined by extendedFluctuation in the colvar. Coupling
should be somewhat loose for faster exploration and convergence, but strong enough that the bias does
help overcome barriers along the colvar ξ .[11] Distribution of the colvar may be assessed by plotting its
histogram, which is written to the output.zcount file in every eABF simulation. Note that a histogram
bias (6.9) applied to an extended-Lagrangian colvar will access the extended degree of freedom λ , not the
original colvar ξ ; however, the joint histogram may be explicitly requested by listing the name of the colvar
twice in a row within the colvars parameter of the histogram block.
The eABF PMF is that of the coordinate λ , it is not exactly the free energy profile of ξ . That quantity
can be calculated based on the CZAR estimator.

6.2.1 CZAR estimator of the free energy

The corrected z-averaged restraint (CZAR) estimator is described in detail in reference [11]. It is computed
automatically in eABF simulations, regardless of the number of colvars involved. Note that ABF may also
be applied on a combination of extended and non-extended colvars; in that case, CZAR still provides an
unbiased estimate of the free energy gradient.
CZAR estimates the free energy gradient as:
1 d ln ρ̃(z)
A0 (z) = − + k(hλ iz − z). (18)
β dz

47
where z = ξ (q) is the colvar, λ is the extended variable harmonically coupled to z with a force constant k,
and ρ̃(z) is the observed distribution (histogram) of z, affected by the eABF bias.
Parameters for the CZAR estimator are:

• CZARestimator h Calculate CZAR estimator of the free energy? i

Context: abf
Acceptable values: boolean
Default value: yes
Description: This option is only available when ABF is performed on extended-Lagrangian colvars.
When enabled, it triggers calculation of the free energy following the CZAR estimator.

• writeCZARwindowFile h Write internal data from CZAR to a separate file? i

Context: abf
Acceptable values: boolean
Default value: no
Description: When this option is enabled, eABF simulations will write a file containing the z-
averaged restraint force under the name output.zgrad. The same information is always included in
the colvars state file, which is sufficient for restarting an eABF simulation. These separate file is
only useful when joining adjacent windows from a stratified eABF simulation, either to continue the
simulation in a broader window or to compute a CZAR estimate of the PMF over the full range of the
coordinate(s).

Similar to ABF, the CZAR estimator produces two output files in multicolumn text format:

• output.czar.grad: current estimate of the free energy gradient (grid), in multicolumn;

• output.czar.pmf: only for one-dimensional calculations, integrated free energy profile or PMF.

The sampling histogram associated with the CZAR estimator is the z-histogram, which is written in the file
output.zcount.

6.3 Metadynamics
The metadynamics method uses a history-dependent potential [12] that generalizes to any type of colvars
the conformational flooding [13] and local elevation [14] methods, originally formulated to use as colvars
the principal components of a covariance matrix or a set of dihedral angles, respectively. The metadynamics
potential on the colvars ξ = (ξ1 , ξ2 , . . . , ξNcv ) is defined as:
!
t 0 <t Ncv
(ξi (t) − ξi (t 0 ))2
Vmeta (ξ (t)) = ∑ W ∏ exp − 2σξ2i
, (19)
t 0 =δt,2δt,... i=1

where Vmeta is the history-dependent potential acting on the current values of the colvars ξ , and depends
only parametrically on the previous values of the colvars. Vmeta is constructed as a sum of Ncv -dimensional
repulsive Gaussian “hills”, whose height is a chosen energy constant W , and whose centers are the previously
explored configurations (ξ (δt), ξ (2δt), . . .).
During the simulation, the system evolves towards the nearest minimum of the “effective” potential of
mean force Ã(ξ ), which is the sum of the “real” underlying potential of mean force A(ξ ) and the the meta-
dynamics potential, Vmeta (ξ ). Therefore, at any given time the probability of observing the configuration ξ ∗
is proportional to exp −Ã(ξ ∗ )/κB T : this is also the probability that a new Gaussian “hill” is added at that

48
configuration. If the simulation is run for a sufficiently long time, each local minimum is canceled out by
the sum of the Gaussian “hills”. At that stage the “effective” potential of mean force Ã(ξ ) is constant, and
−Vmeta (ξ ) is an accurate estimator of the “real” potential of mean force A(ξ ), save for an additive constant:

A(ξ ) ' −Vmeta (ξ ) + K (20)

Assuming that the set of collective variables includes all relevant degrees of freedom, the predicted
error of the estimate is a simple function of the correlation times of the colvars τξi , and of the user-defined
parameters W , σξi and δt [15]. In typical applications, a good rule of thumb can be to choose the ratio
W /δt much smaller than κB T /τξ , where τξ is the longest among ξ ’s correlation times: σξi then dictates
the resolution of the calculated PMF.

6.3.1 Basic syntax

To enable a metadynamics calculation, a metadynamics {...} block must be defined in the Colvars config-
uration file. Its mandatory keywords are colvars, which lists all the variables involved, hillWeight, which
specifies the weight parameter W , and hillWidth, which defines the Gaussian width 2σξ as a number of
grid points.

• name: see definition of name in sec. 6 (biasing and analysis methods)

• colvars: see definition of colvars in sec. 6 (biasing and analysis methods)

• outputEnergy: see definition of outputEnergy in sec. 6 (biasing and analysis methods)

• writeTIPMF: see definition of writeTIPMF in sec. 6 (biasing and analysis methods)

• writeTISamples: see definition of writeTISamples in sec. 6 (biasing and analysis methods)

• hillWeight h Height of each hill (unit of energy specified by units) i

Context: metadynamics
Acceptable values: positive decimal
Description: This option sets the height W of the Gaussian hills that are added during this run.
Lower values provide more accurate sampling of the system’s degrees of freedom at the price of
longer simulation times to complete a PMF calculation based on metadynamics.

• hillWidth h Width of a Gaussian hill, measured in number of grid points i

Context: metadynamics
Acceptable values: positive decimal
Description: The value of this keyword is the Gaussian width 2σξi , expressed in number of grid
points: the grid spacing is determined by width. The values of the parameter σξi for each variable
ξi inits physical units are printed by LAMMPS at initialization time. Values between 1 and 3 are
recommended: smaller values fail to adequately interpolate each Gaussian [1], while larger values
may be unable to account for steep free-energy gradients.

• newHillFrequency h Frequency of hill creation i

Context: metadynamics
Acceptable values: positive integer
Default value: 1000
Description: This option sets the number of steps after which a new Gaussian hill is added to

49
 the metadynamics potential. The product of this number and the integration time-step defines the
parameter δt in eq. 19. Higher values provide more accurate statistical sampling, at the price of
longer simulation times to complete a PMF calculation.

6.3.2 Output files

When interpolating grids are enabled (default behavior), the PMF is written by default every colvarsRestartFrequency
steps to the file output.pmf. The following two options allow to disable or control this behavior and to track
statistical convergence:

• writeFreeEnergyFile h Periodically write the PMF for visualization i

Context: metadynamics
Acceptable values: boolean
Default value: on
Description: When useGrids and this option are on, the PMF is written every colvarsRestartFrequency
steps.

• keepFreeEnergyFiles h Keep all the PMF files i

Context: metadynamics
Acceptable values: boolean
Default value: off
Description: When writeFreeEnergyFile and this option are on, the step number is included in
the file name, thus generating a series of PMF files. Activating this option can be useful to follow
more closely the convergence of the simulation, by comparing PMFs separated by short times.

Note: when Gaussian hills are deposited near the lowerBoundary or upperBoundary and interpolating
grids are used (default behavior), their truncation can give rise to accumulating errors. In these cases, as a
measure of fault-tolerance all Gaussian hills near the boundaries are included in the output state file, and are
recalculated analytically whenever the variable falls outside the grid’s boundaries. (Such measure protects
the accuracy of the calculation, and can only be disabled by hardLowerBoundary or hardUpperBoundary.)
To avoid gradual loss of performance and growth of the state file, either one of the following solutions is
recommended:

• enabling the option expandBoundaries, so that the grid’s boundaries are automatically recalculated
whenever necessary; the resulting .pmf will have its abscissas expanded accordingly;

• applying a harmonicWalls bias with the wall locations well within the interval delimited by lowerBoundary
and upperBoundary.

6.3.3 Performance tuning

The following options control the computational cost of metadynamics calculations, but do not affect results.
Default values are chosen to minimize such cost with no loss of accuracy.

• useGrids h Interpolate the hills with grids i

Context: metadynamics

50
 Acceptable values: boolean
Default value: on
Description: This option discretizes all hills for improved performance, accumulating their en-
ergy and their gradients on two separate grids of equal spacing. Grids are defined by the values
of lowerBoundary, upperBoundary and width for each colvar. Currently, this option is imple-
mented for all types of variables except the non-scalar types (distanceDir or orientation). If
expandBoundaries is defined in one of the colvars, grids are automatically expanded along the di-
rection of that colvar.

• rebinGrids h Recompute the grids when reading a state file i

Context: metadynamics
Acceptable values: boolean
Default value: off
Description: When restarting from a state file, the grid’s parameters (boundaries and widths) saved
in the state file override those in the configuration file. Enabling this option forces the grids to match
those in the current configuration file.

6.3.4 Well-tempered metadynamics

The following options define the configuration for the “well-tempered” metadynamics approach [16]:

• wellTempered h Perform well-tempered metadynamics i

Context: metadynamics
Acceptable values: boolean
Default value: off
Description: If enabled, this flag causes well-tempered metadynamics as described by Barducci et
al.[16] to be performed, rather than standard metadynamics. The parameter biasTemperature is then
required.This feature was contributed by Li Li (Luthey-Schulten group, Departement of Chemistry,
UIUC).

• biasTemperature h Temperature bias for well-tempered metadynamics i

Context: metadynamics
Acceptable values: positive decimal
Description: When running metadynamics in the long time limit, collective variable space is sampled
to a modified temperature T + ∆T . In conventional metadynamics, the temperature “boost” ∆T would
constantly increases with time. Instead, in well-tempered metadynamics ∆T must be defined by the
user via biasTemperature. The written PMF includes the scaling factor (T +∆T )/∆T [16]. A careful
choice of ∆T determines the sampling and convergence rate, and is hence crucial to the success of a
well-tempered metadynamics simulation.

6.3.5 Multiple-replicas metadynamics

The following options define metadynamics calculations with more than one replica:

• multipleReplicas h Multiple replicas metadynamics i

Context: metadynamics

51
 Acceptable values: boolean
Default value: off
Description: If this option is on, multiple (independent) replica of the same system can be run at the
same time, and their hills will be combined to obtain a single PMF [17]. Replicas are identified by
the value of replicaID. Communication is done by files: each replica must be able to read the files
created by the others, whose paths are communicated through the file replicasRegistry. This file,
and the files listed in it, are read every replicaUpdateFrequency steps. Every time the colvars state
file is written (colvarsRestartFrequency), the file:
“output.colvars.name.replicaID.state” is also written, containing the state of the metadynamics
bias for replicaID. In the time steps between colvarsRestartFrequency, new hills are temporarily
written to the file:
“output.colvars.name.replicaID.hills”, which serves as communication buffer. These files are
only required for communication, and may be deleted after a new MD run is started with a different
outputName.

• replicaID h Set the identifier for this replica i

Context: metadynamics
Acceptable values: string
Description: If multipleReplicas is on, this option sets a unique identifier for this replica. All
replicas should use identical collective variable configurations, except for the value of this option.

• replicasRegistry h Multiple replicas database file i

Context: metadynamics
Acceptable values: UNIX filename
Default value: “name.replica files.txt”
Description: If multipleReplicas is on, this option sets the path to the replicas’ database file.

• replicaUpdateFrequency h How often hills are communicated between replicas i

Context: metadynamics
Acceptable values: positive integer
Default value: newHillFrequency
Description: If multipleReplicas is on, this option sets the number of steps after which each
replica (re)reads the other replicas’ files. The lowest meaningful value of this number is newHillFrequency.
If access to the file system is significantly affecting the simulation performance, this number can be in-
creased, at the price of reduced synchronization between replicas. Values higher than colvarsRestartFrequency
may not improve performance significantly.

• dumpPartialFreeEnergyFile h Periodically write the contribution to the PMF from this replica i
Context: metadynamics
Acceptable values: boolean
Default value: on
Description: When multipleReplicas is on, the file output.pmf contains the combined PMF from
all replicas, provided that useGrids is on (default). Enabling this option produces an additional file
output.partial.pmf, which can be useful to quickly monitor the contribution of each replica to the
PMF.

52
6.3.6 Compatibility and post-processing
The following options may be useful only for applications that go beyond the calculation of a PMF by
metadynamics:
• name h Name of this metadynamics instance i
Context: metadynamics
Acceptable values: string
Default value: “meta” + rank number
Description: This option sets the name for this metadynamics instance. While it is not advisable to
use more than one metadynamics instance within the same simulation, this allows to distinguish each
instance from the others. If there is more than one metadynamics instance, the name of this bias is
included in the metadynamics output file names, such as e.g. the .pmf file.
• keepHills h Write each individual hill to the state file i
Context: metadynamics
Acceptable values: boolean
Default value: off
Description: When useGrids and this option are on, all hills are saved to the state file in their
analytic form, alongside their grids. This makes it possible to later use exact analytic Gaussians
for rebinGrids. To only keep track of the history of the added hills, writeHillsTrajectory is
preferable.
• writeHillsTrajectory h Write a log of new hills i
Context: metadynamics
Acceptable values: boolean
Default value: off
Description: If this option is on, a logfile is written by the metadynamics bias, with the name
“output.colvars.<name>.hills.traj”, which can be useful to follow the time series of the hills.
When multipleReplicas is on, its name changes to
“output.colvars.<name>.<replicaID>.hills.traj”. This file can be used to quickly visualize
the positions of all added hills, in case newHillFrequency does not coincide with colvarsRestartFrequency.

6.4 Harmonic restraints

The harmonic biasing method may be used to enforce fixed or moving restraints, including variants of
Steered and Targeted MD. Within energy minimization runs, it allows for restrained minimization, e.g. to
calculate relaxed potential energy surfaces. In the context of the Colvars module, harmonic potentials are
meant according to their textbook definition:
ξ − ξ0 2
 
1
V (ξ ) = k (21)
2 wξ
Note that this differs from harmonic bond and angle potentials in common force fields, where the factor of
one half is typically omitted, resulting in a non-standard definition of the force constant.
The formula above includes the characteristic length scale wξ of the colvar ξ (keyword lowerBoundary)
to allow the definition of a multi-dimensional restraint with a unified force constant:
1 M ξi − ξ0 2
 
V (ξ1 , . . . , ξM ) = k ∑ (22)
2 i=1 wξ

53
 If one-dimensional or homogeneous multi-dimensional restraints are defined, and there are no other uses
for the parameter wξ , the parameter width can be left at its default value of 1.
A harmonic restraint is set up by a harmonic {...} block, which may contain (in addition to the
standard option colvars) the following keywords:

• name: see definition of name in sec. 6 (biasing and analysis methods)

• colvars: see definition of colvars in sec. 6 (biasing and analysis methods)

• outputEnergy: see definition of outputEnergy in sec. 6 (biasing and analysis methods)

• writeTIPMF: see definition of writeTIPMF in sec. 6 (biasing and analysis methods)

• writeTISamples: see definition of writeTISamples in sec. 6 (biasing and analysis methods)

• forceConstant h Scaled force constant (unit of energy specified by units) i

Context: harmonic
Acceptable values: positive decimal
Default value: 1.0
Description: This option defines a scaled force constant k for the harmonic potential (eq. 22). To
ensure consistency for multidimensional restraints, it is divided internally by the square of the specific
width of each variable (which is 1 by default). This makes all values effectively dimensionless and
of commensurate size. For instance, setting a scaled force constant of 10 kcal/mol acting on two
variables, an angle with a width of 5 degrees and a distance with a width of 0.5 Å, will apply actual
force constants of 0.4 kcal/mol×degree−2 for the angle and 40 kcal/mol/Å2 for the distance. The
values of the actual force constants are always printed when the restraint is defined.

• centers h Initial harmonic restraint centers i

Context: harmonic
Acceptable values: space-separated list of colvar values
Description: The centers (equilibrium values) of the restraint, ξ0 , are entered here. The number of
values must be the number of requested colvars. Each value is a decimal number if the corresponding
colvar returns a scalar, a “(x, y, z)” triplet if it returns a unit vector or a vector, and a “(q0, q1,
q2, q3)” quadruplet if it returns a rotational quaternion. If a colvar has periodicities or symmetries,
its closest image to the restraint center is considered when calculating the harmonic potential.

Tip: A complex set of restraints can be applied to a system, by defining several colvars, and applying
one or more harmonic restraints to different groups of colvars. In some cases, dozens of colvars can be
defined, but their value may not be relevant: to limit the size of the colvars trajectory file, it may be wise to
disable outputValue for such “ancillary” variables, and leave it enabled only for “relevant” ones.

6.4.1 Moving restraints: steered molecular dynamics

The following options allow to change gradually the centers of the harmonic restraints during a simulations.
When the centers are changed continuously, a steered MD in a collective variable space is carried out.

• targetCenters h Steer the restraint centers towards these targets i

Context: harmonic
Acceptable values: space-separated list of colvar values
Description: When defined, the current centers will be moved towards these values during the

54
 simulation. By default, the centers are moved over a total of targetNumSteps steps by a linear inter-
polation, in the spirit of Steered MD. If targetNumStages is set to a nonzero value, the change is per-
formed in discrete stages, lasting targetNumSteps steps each. This second mode may be used to sam-
ple successive windows in the context of an Umbrella Sampling simulation. When continuing a simu-
lation run, the centers specified in the configuration file <colvarsConfig> are overridden by those
saved in the restart file <colvarsInput>. To perform Steered MD in an arbitrary space of colvars,
it is sufficient to use this option and enable outputAccumulatedWork and/or outputAppliedForce
within each of the colvars involved.
• targetNumSteps h Number of steps for steering i
Context: harmonic
Acceptable values: positive integer
Description: In single-stage (continuous) transformations, defines the number of MD steps required
to move the restraint centers (or force constant) towards the values specified with targetCenters or
targetForceConstant. After the target values have been reached, the centers (resp. force constant)
are kept fixed. In multi-stage transformations, this sets the number of MD steps per stage.
• outputCenters h Write the current centers to the trajectory file i
Context: harmonic
Acceptable values: boolean
Default value: off
Description: If this option is chosen and colvarsTrajFrequency is not zero, the positions of the
restraint centers will be written to the trajectory file during the simulation. This option allows to
conveniently extract the PMF from the colvars trajectory files in a steered MD calculation.

Note on restarting moving restraint simulations: Information about the current step and stage of a
simulation with moving restraints is stored in the restart file (state file). Thus, such simulations can be run
in several chunks, and restarted directly using the same colvars configuration file. In case of a restart, the
values of parameters such as targetCenters, targetNumSteps, etc. should not be changed manually.

6.4.2 Moving restraints: umbrella sampling

The centers of the harmonic restraints can also be changed in discrete stages: in this cases a one-dimensional
umbrella sampling simulation is performed. The sampling windows in simulation are calculated in sequence.
The colvars trajectory file may then be used both to evaluate the correlation times between consecutive
windows, and to calculate the frequency distribution of the colvar of interest in each window. Furthermore,
frequency distributions on a predefined grid can be automatically obtained by using the histogram bias (see
6.9).
To activate an umbrella sampling simulation, the same keywords as in the previous section can be used,
with the addition of the following:
• targetNumStages h Number of stages for steering i
Context: harmonic
Acceptable values: non-negative integer
Default value: 0
Description: If non-zero, sets the number of stages in which the restraint centers or force constant
are changed to their target values. If zero, the change is continuous. Each stage lasts targetNumSteps
MD steps. To sample both ends of the transformation, the simulation should be run for targetNumSteps
× (targetNumStages + 1).

55
6.4.3 Changing force constant
The force constant of the harmonic restraint may also be changed to equilibrate [18].

• targetForceConstant h Change the force constant towards this value i

Context: harmonic
Acceptable values: positive decimal
Description: When defined, the current forceConstant will be moved towards this value during the
simulation. Time evolution of the force constant is dictated by the targetForceExponent parameter
(see below). By default, the force constant is changed smoothly over a total of targetNumSteps steps.
This is useful to introduce or remove restraints in a progressive manner. If targetNumStages is set
to a nonzero value, the change is performed in discrete stages, lasting targetNumSteps steps each.
This second mode may be used to compute the conformational free energy change associated with the
restraint, within the FEP or TI formalisms. For convenience, the code provides an estimate of the free
energy derivative for use in TI. A more complete free energy calculation (particularly with regard to
convergence analysis), while not handled by the Colvars module, can be performed by post-processing
the colvars trajectory, if colvarsTrajFrequency is set to a suitably small value. It should be noted,
however, that restraint free energy calculations may be handled more efficiently by an indirect route,
through the determination of a PMF for the restrained coordinate.[18]

• targetForceExponent h Exponent in the time-dependence of the force constant i

Context: harmonic
Acceptable values: decimal equal to or greater than 1.0
Default value: 1.0
Description: Sets the exponent, α, in the function used to vary the force constant as a function
of time. The force is varied according to a coupling parameter λ , raised to the power α: kλ =
k0 + λ α (k1 − k0 ), where k0 , kλ , and k1 are the initial, current, and final values of the force constant.
The parameter λ evolves linearly from 0 to 1, either smoothly, or in targetNumStages equally spaced
discrete stages, or according to an arbitrary schedule set with lambdaSchedule. When the initial value
of the force constant is zero, an exponent greater than 1.0 distributes the effects of introducing the
restraint more smoothly over time than a linear dependence, and ensures that there is no singularity in
the derivative of the restraint free energy with respect to lambda. A value of 4 has been found to give
good results in some tests.

• targetEquilSteps h Number of steps discarded from TI estimate i

Context: harmonic
Acceptable values: positive integer
Description: Defines the number of steps within each stage that are considered equilibration and
discarded from the restraint free energy derivative estimate reported reported in the output.

• lambdaSchedule h Schedule of lambda-points for changing force constant i

Context: harmonic
Acceptable values: list of real numbers between 0 and 1
Description: If specified together with targetForceConstant, sets the sequence of discrete λ values
that will be used for different stages.

56
6.5 Computing the work of a changing restraint
If the restraint centers or force constant are changed continuosly (targetNumStages undefined) it is possible
to record the net work performed by the changing restraint:

• outputAccumulatedWork h Write the accumulated work of the changing restraint to the Colvars
trajectory file i
Context: harmonic
Acceptable values: boolean
Default value: off
Description: If targetCenters or targetForceConstant are defined and this option is enabled,
the accumulated work from the beginning of the simulation will be written to the trajectory file
(colvarsTrajFrequency must be non-zero). When the simulation is continued from a state file, the
previously accumulated work is included in the integral. This option allows to conveniently extract
the estimated PMF of a steered MD calculation (when targetCenters is used), or of other simulation
protocols.

6.6 Harmonic wall restraints

The harmonicWalls {...} bias is closely related to the harmonic bias (see 6.4), with the following two
differences: (i) instead of a center a lower wall and/or an upper wall are defined, outside of which the bias
implements a half-harmonic potential;

ξ −ξupper 2
  
1

 2
 k wξ if ξ > ξupper
V (ξ ) = 0 if ξlower ≤ ξ ≥ ξupper (23)
  2
 1 k ξ −ξlower

if ξ < ξ
2 wξ lower

where ξlower and ξupper are the lower and upper wall thresholds, respectively; (ii) because an interval between
two walls is defined, only scalar variables can be used (but any number of variables can be defined, and the
wall bias is intrinsically multi-dimensional).
Note: this bias replaces the keywords lowerWall, lowerWallConstant, upperWall and upperWallConstant
defined in the colvar context (see 4). These keywords are still supported, but are deprecated for future uses.
The harmonicWalls bias implements the following options:

• name: see definition of name in sec. 6 (biasing and analysis methods)

• colvars: see definition of colvars in sec. 6 (biasing and analysis methods)

• outputEnergy: see definition of outputEnergy in sec. 6 (biasing and analysis methods)

• writeTIPMF: see definition of writeTIPMF in sec. 6 (biasing and analysis methods)

• writeTISamples: see definition of writeTISamples in sec. 6 (biasing and analysis methods)

• lowerWalls h Position of the lower wall i

Context: colvar
Acceptable values: Space-separated list of decimals
Description: Defines the values ξlower below which a confining restraint on the colvar is applied to
each colvar ξ .

57
 • upperWalls h Position of the lower wall i
Context: colvar
Acceptable values: Space-separated list of decimals
Description: Defines the values ξupper above which a confining restraint on the colvar is applied to
each colvar ξ .

• forceConstant: see definition of forceConstant in sec. 6.4 (Harmonic restraints)

• lowerWallConstant h Force constant for the lower wall i

Context: harmonicWalls
Acceptable values: positive decimal
Default value: forceConstant
Description: When both sets of walls are defined (lower and upper), this keyword allows setting
different force constants for them. The force constant reported in the output as “k”, and used in the
change of force constant scheme, is the geometric mean of the two.

• upperWallConstant: analogous to lowerWallConstant

• targetForceConstant: see definition of targetForceConstant in sec. 6.4 (Harmonic restraints)

• targetForceConstant h Change the force constant(s) towards this value i

Context: harmonicWalls
Acceptable values: positive decimal
Description: This keyword allows changing either one or both of the wall force constants over time.
In the case that lowerWallConstant and upperWallConstant have the same value, the behavior
of this keyword is identical to the corresponding keyword in the harmonic restraint; otherwise, the
change schedule is applied to the geometric mean of the two constant. When only one set of walls
is defined (lowerWall or upperWalls), only the respective force constant is changed. Note: if only
one of the two force constants is meant to change over time, it is possible to use two instances of
harmonicWalls, and apply the changing schedule only to one of them.

• targetNumSteps: see definition of targetNumSteps in sec. 6.4 (Harmonic restraints)

• targetForceExponent: see definition of targetForceExponent in sec. 6.4 (Harmonic restraints)

• targetEquilSteps: see definition of targetEquilSteps in sec. 6.4 (Harmonic restraints)

• targetNumStages: see definition of targetNumStages in sec. 6.4 (Harmonic restraints)

• lambdaSchedule: see definition of lambdaSchedule in sec. 6.4 (Harmonic restraints)

• outputAccumulatedWork: see definition of outputAccumulatedWork in sec. 6.4 (Harmonic re-

straints)

6.7 Linear restraints

The linear restraint biasing method is used to minimally bias a simulation. There is generally a unique
strength of bias for each CV center, which means you must know the bias force constant specifically for the
center of the CV. This force constant may be found by using experiment directed simulation described in
section 6.8. Please cite Pitera and Chodera when using [19].

58
 • name: see definition of name in sec. 6 (biasing and analysis methods)

• colvars: see definition of colvars in sec. 6 (biasing and analysis methods)

• outputEnergy: see definition of outputEnergy in sec. 6 (biasing and analysis methods)

• forceConstant h Scaled force constant (unit of energy specified by units) i

Context: linear
Acceptable values: positive decimal
Default value: 1.0
Description: This option defines a scaled force constant for the linear bias. To ensure consistency for
multidimensional restraints, it is divided internally by the specific width of each variable (which is 1
by default), so that all variables are effectively dimensionless and of commensurate size. The values
of the actual force constants are always printed when the restraint is defined.

• centers h Initial linear restraint centers i

Context: linear
Acceptable values: space-separated list of colvar values
Description: These are analogous to the centers keyword of the harmonic restraint. Although they
do not affect dynamics, they are here necessary to ensure a well-defined energy for the linear bias.

• writeTIPMF: see definition of writeTIPMF in sec. 6 (biasing and analysis methods)

• writeTISamples: see definition of writeTISamples in sec. 6 (biasing and analysis methods)

• targetForceConstant: see definition of targetForceConstant in sec. 6.4 (Harmonic restraints)

• targetNumSteps: see definition of targetNumSteps in sec. 6.4 (Harmonic restraints)

• targetForceExponent: see definition of targetForceExponent in sec. 6.4 (Harmonic restraints)

• targetEquilSteps: see definition of targetEquilSteps in sec. 6.4 (Harmonic restraints)

• targetNumStages: see definition of targetNumStages in sec. 6.4 (Harmonic restraints)

• lambdaSchedule: see definition of lambdaSchedule in sec. 6.4 (Harmonic restraints)

• outputAccumulatedWork: see definition of outputAccumulatedWork in sec. 6.4 (Harmonic re-

straints)

6.8 Adaptive Linear Bias/Experiment Directed Simulation

Experiment directed simulation applies a linear bias with a changing force constant. Please cite White and
Voth [20] when using this feature. As opposed to that reference, the force constant here is scaled by the
width corresponding to the biased colvar. In White and Voth, each force constant is scaled by the colvars
set center. The bias converges to a linear bias, after which it will be the minimal possible bias. You may
also stop the simulation, take the median of the force constants (ForceConst) found in the colvars trajectory
file, and then apply a linear bias with that constant. All the notes about units described in sections 6.7 and
6.4 apply here as well. This is not a valid simulation of any particular statistical ensemble and is only
an optimization algorithm until the bias has converged.

59
• name: see definition of name in sec. 6 (biasing and analysis methods)

• colvars: see definition of colvars in sec. 6 (biasing and analysis methods)

• centers h Collective variable centers i

Context: alb
Acceptable values: space-separated list of colvar values
Description: The desired center (equilibrium values) which will be sought during the adaptive linear
biasing. The number of values must be the number of requested colvars. Each value is a decimal
number if the corresponding colvar returns a scalar, a “(x, y, z)” triplet if it returns a unit vector
or a vector, and a “q0, q1, q2, q3)” quadruplet if it returns a rotational quaternion. If a colvar has
periodicities or symmetries, its closest image to the restraint center is considered when calculating the
linear potential.

• updateFrequency h The duration of updates i

Context: alb
Acceptable values: An integer
Description: This is, N, the number of simulation steps to use for each update to the bias. This
determines how long the system requires to equilibrate after a change in force constant (N/2), how
long statistics are collected for an iteration (N/2), and how quickly energy is added to the system
(at most, A/2N, where A is the forceRange). Until the force constant has converged, the method
as described is an optimization procedure and not an integration of a particular statistical ensemble.
It is important that each step should be uncorrelated from the last so that iterations are independent.
Therefore, N should be at least twice the autocorrelation time of the collective variable. The system
should also be able to dissipate energy as fast as N/2, which can be done by adjusting thermostat
parameters. Practically, N has been tested successfully at significantly shorter than the autocorrelation
time of the collective variables being biased and still converge correctly.

• forceRange h The expected range of the force constant in units of energy i

Context: alb
Acceptable values: A space-separated list of decimal numbers
Default value: 3 kb T
Description: This is largest magnitude of the force constant which one expects. If this parameter is
too low, the simulation will not converge. If it is too high the simulation will waste time exploring
values that are too large. A value of 3 kb T has worked well in the systems presented as a first choice.
This parameter is dynamically adjusted over the course of a simulation. The benefit is that a bad guess
for the forceRange can be corrected. However, this can lead to large amounts of energy being added
over time to the system. To prevent this dynamic update, add hardForceRange yes as a parameter

• rateMax h The maximum rate of change of force constant i

Context: alb
Acceptable values: A list of space-separated real numbers
Description: This optional parameter controls how much energy is added to the system from this
bias. Tuning this separately from the updateFrequency and forceRange can allow for large bias
changes but with a low rateMax prevents large energy changes that can lead to instability in the
simulation.

60
6.9 Multidimensional histograms
The histogram feature is used to record the distribution of a set of collective variables in the form of a
N-dimensional histogram.
As with any other biasing and analysis method, when a histogram is applied to an extended-system
colvar (4.9), it accesses the value of the fictitious coordinate rather than that of the “true” colvar. A joint
histogram of the “true” colvar and the fictitious coordinate may be obtained by specifying the colvar name
twice in a row in the colvars parameter: the first instance will be understood as the “true” colvar, and the
second, as the fictitious coordinate.
A histogram block may define the following parameters:

• name: see definition of name in sec. 6 (biasing and analysis methods)

• colvars: see definition of colvars in sec. 6 (biasing and analysis methods)

• outputFreq h Frequency (in timesteps) at which the histogram files are refreshed i
Context: histogram
Acceptable values: positive integer
Default value: colvarsRestartFrequency
Description: The histogram data are written to files at the given time interval. A value of 0 disables
the creation of these files (note: all data to continue a simulation are still included in the state file).

• outputFile h Write the histogram to a file i

Context: histogram
Acceptable values: UNIX filename
Default value: output.<name>.dat
Description: Name of the file containing histogram data (multicolumn format), which is written
every outputFreq steps. For the special case of 2 variables, Gnuplot may be used to visualize this
file.

• outputFileDX h Write the histogram to a file i

Context: histogram
Acceptable values: UNIX filename
Default value: output.<name>.dat
Description: Name of the file containing histogram data (OpenDX format), which is written every
outputFreq steps. For the special case of 3 variables, VMD may be used to visualize this file.

• gatherVectorColvars h Treat vector variables as multiple observations of a scalar variable? i

Context: histogram
Acceptable values: UNIX filename
Default value: off
Description: When this is set to on, the components of a multi-dimensional colvar (e.g. one based
on cartesian, distancePairs, or a vector of scalar numbers given by scriptedFunction) are
treated as multiple observations of a scalar variable. This results in the histogram being accumulated
multiple times for each simulation step). When multiple vector variables are included in histogram,
these must have the same length because their components are accumulated together. For example,
if ξ , λ and τ are three variables of dimensions 5, 5 and 1, respectively, for each iteration 5 triplets
(ξi , λi , τ) (i = 1, . . . 5) are accumulated into a 3-dimensional histogram.

• weights h Treat vector variables as multiple observations of a scalar variable? i

Context: histogram

61
 Acceptable values: list of space-separated decimals
Default value: all weights equal to 1
Description: When gatherVectorColvars is on, the components of each multi-dimensional colvar
are accumulated with a different weight. For example, if x and y are two distinct cartesian variables
defined on the same group of atoms, the corresponding 2D histogram can be weighted on a per-atom
basis in the definition of histogram.

6.9.1 Grid definition for multidimensional histograms

Like the ABF and metadynamics biases, histogram uses the parameters lowerBoundary, upperBoundary,
and width to define its grid. These values can be overridden if a configuration block histogramGrid {
. . . } is provided inside the configuration of histogram. The options supported inside this configuration
block are:

• lowerBoundaries h Lower boundaries of the grid i

Context: histogramGrid
Acceptable values: list of space-separated decimals
Description: This option defines the lower boundaries of the grid, overriding any values defined
by the lowerBoundary keyword of each colvar. Note that when gatherVectorColvars is on, each
vector variable is automatically treated as a scalar, and a single value should be provided for it.

• upperBoundaries: analogous to lowerBoundaries

• widths: analogous to lowerBoundaries

6.10 Probability distribution-restraints

The histogramRestraint bias implements a continuous potential of many variables (or of a single high-
dimensional variable) aimed at reproducing a one-dimensional statistical distribution that is provided by the
user. The M variables (ξ1 , . . . , ξM ) are interpreted as multiple observations of a random variable ξ with
unknown probability distribution. The potential is minimized when the histogram h(ξ ), estimated as a sum
of Gaussian functions centered at (ξ1 , . . . , ξM ), is equal to the reference histogram h0 (ξ ):

1
Z
V (ξ1 , . . . , ξM ) = k (h(ξ ) − h0 (ξ ))2 dξ (24)
2
M
(ξ − ξi )2
 
1
h(ξ ) = √ ∑ exp − 2σ 2 (25)
M 2πσ 2 i=1
When used in combination with a distancePairs multi-dimensional variable, this bias implements the
refinement algorithm against ESR/DEER experiments published by Shen et al [21].
This bias behaves similarly to the histogram bias with the gatherVectorColvars option, with the im-
portant difference that all variables are gathered, resulting in a one-dimensional histogram. Future versions
will include support for multi-dimensional histograms.
The list of options is as follows:

• name: see definition of name in sec. 6 (biasing and analysis methods)

62
• colvars: see definition of colvars in sec. 6 (biasing and analysis methods)
• outputEnergy: see definition of outputEnergy in sec. 6 (biasing and analysis methods)
• lowerBoundary h Lower boundary of the colvar grid i
Context: histogramRestraint
Acceptable values: decimal
Description: Defines the lowest end of the interval where the reference distribution h0 (ξ ) is defined.
Exactly one value must be provided, because only one-dimensional histograms are supported by the
current version.
• upperBoundary: analogous to lowerBoundary
• width h Width of the colvar grid i
Context: histogramRestraint
Acceptable values: positive decimal
Description: Defines the spacing of the grid where the reference distribution h0 (ξ ) is defined.
• gaussianSigma h Standard deviation of the approximating Gaussian i
Context: histogramRestraint
Acceptable values: positive decimal
Default value: 2 × width
Description: Defines the parameter σ in eq. 25.
• forceConstant h Force constant (unit of energy specified by units) i
Context: histogramRestraint
Acceptable values: positive decimal
Default value: 1.0
Description: Defines the parameter k in eq. 24.
• refHistogram h Reference histogram h0 (ξ ) i
Context: histogramRestraint
Acceptable values: space-separated list of M positive decimals
Description: Provides the values of h0 (ξ ) consecutively. The mid-point convention is used, i.e. the
first point that should be included is for ξ = lowerBoundary+width/2. If the integral of h0 (ξ ) is not
normalized to 1, h0 (ξ ) is rescaled automatically before use.
• refHistogramFile h Reference histogram h0 (ξ ) i
Context: histogramRestraint
Acceptable values: UNIX file name
Description: Provides the values of h0 (ξ ) as contents of the corresponding file (mutually exclusive
with refHistogram). The format is that of a text file, with each line containing the space-separated
values of ξ and h0 (ξ ). The same numerical conventions as refHistogram are used.
• writeHistogram h Periodically write the instantaneous histogram h(ξ ) i
Context: metadynamics
Acceptable values: boolean
Default value: off
Description: If on, the histogram h(ξ ) is written every colvarsRestartFrequency steps to a file
with the name output.<name>.hist.dat This is useful to diagnose the convergence of h(ξ ) against
h0 (ξ ).

63
7 Syntax changes from older versions
The following is a list of syntax changes in Colvars since its first release. Many of the older keywords are
still recognized by the current code, thanks to specific compatibility code. This is not a list of new features:
its primary purpose is to make you aware of those improvements that affect the use of old configuration files
with new versions of the code.
Note: if you are using any of the NAMD and VMD tutorials:
https://www.ks.uiuc.edu/Training/Tutorials/
please be aware that several of these tutorials are not actively maintained: for those cases, this list will help
you reconcile any inconsistencies.

• Colvars version 2016-06-09 or later (LAMMPS version 15Sep2016 or later).

The legacy keyword refPositionsGroup has been renamed fittingGroup for clarity (the legacy
version is still supported).

• Colvars version 2016-08-10 or later (LAMMPS version 15Sep2016 or later).

“System forces” have been replaced by “total forces” (see for example outputTotalForce). See the
following page for more information:
https://colvars.github.io/README-totalforce.html

• Colvars version 2017-01-09 or later (LAMMPS version 10Mar2017 or later).

A new type of restraint, harmonicWalls (see 6.6), replaces and improves upon the legacy keywords
lowerWall and upperWall: these are still supported as short-hands.

• Colvars version 2018-11-15 or later (LAMMPS version 23Nov2018 or later).

The global analysis keyword has been discontinued: specific analysis tasks are controlled directly
by the keywords corrFunc and runAve, which continue to remain off by default.

• Deprecation warning for calculations including wall potentials.

The legacy keywords lowerWall and upperWall will stop having default values and will need to
be set explicitly (preferably as part of the harmonicWalls restraint). When using an ABF bias, it
is recommended to set the two walls equal to lowerBoundary and upperBoundary, respectively.
When using a metadynamics bias, it is recommended to set the two walls within lowerBoundary
and upperBoundary. This guarantees that the tails of each Gaussian hill are accounted in the region
between the grid boundaries and the wall potentials. See also expandBoundaries for an automatic
definition of the PMF grid boundaries.

Up-to-date documentation can always be accessed at:

https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html

64
Index
abf extendedTemp, 31
CZARestimator, 47 extendedTimeConstant, 31
applyBias, 44 hardLowerBoundary, 29
colvars, 43 hardUpperBoundary, 29
fullSamples, 43 lowerBoundary, 29
hideJacobian, 43 lowerWalls, 56
historyFreq, 44 name, 9
inputPrefix, 44 outputAppliedForce, 30
maxForce, 43 outputEnergy, 30
name, 43 outputTotalForce, 30
outputFreq, 44 outputValue, 30
updateBias, 44 outputVelocity, 30
writeCZARwindowFile, 47 runAveLength, 33
alb runAveOutputFile, 34
centers, 59 runAveStride, 34
colvars, 59 runAve, 33
forceRange, 59 subtractAppliedForce, 32
name, 59 upperBoundary, 29
rateMax, 59 upperWalls, 57
updateFrequency, 59 width, 29
angle coordNum
forceNoPBC, 15 cutoff3, 17
group1, 15 cutoff, 17
group2, 15 expDenom, 17
group3, 15 expNumer, 17
oneSiteTotalForce, 15 group1, 17
angle, dipoleAngle, dihedral group2CenterOnly, 17
oneSiteTotalForce, 11 group2, 17
cartesian pairListFrequency, 18
atoms, 15 tolerance, 17
colvar dihedral
corrFuncLength, 33 forceNoPBC, 16
corrFuncNormalize, 33 group1, 15
corrFuncOffset, 33 group2, 16
corrFuncOutputFile, 33 group3, 16
corrFuncStride, 33 group4, 16
corrFuncType, 33 oneSiteTotalForce, 16
corrFuncWithColvar, 32 dipoleAngle
corrFunc, 32 forceNoPBC, 15
customFunctionType, 28 group1, 15
customFunction, 28 group2, 15
expandBoundaries, 29 group3, 15
extendedFluctuation, 31 oneSiteTotalForce, 15
extendedLagrangian, 31 distanceDir
extendedLangevinDamping, 32 forceNoPBC, 13

65
 group1, 13 acceptor, 19
group2, 13 cutoff, 19
oneSiteTotalForce, 13 donor, 19
distanceInv expDenom, 19
exponent, 14 expNumer, 19
group1, 14 harmonicWalls
group2, 14 colvars, 56
oneSiteTotalForce, 14 forceConstant, 57
distancePairs lambdaSchedule, 57
forceNoPBC, 14 lowerWallConstant, 57
group1, 14 name, 56
group2, 14 outputAccumulatedWork, 57
distanceVec outputEnergy, 56
forceNoPBC, 13 targetEquilSteps, 57
group1, 13 targetForceConstant, 57
group2, 13 targetForceExponent, 57
oneSiteTotalForce, 13 targetNumStages, 57
distanceXY targetNumSteps, 57
axis, 13 upperWallConstant, 57
forceNoPBC, 13 writeTIPMF, 56
main, 13 writeTISamples, 56
ref2, 13 harmonic
ref, 13 centers, 53
distanceZ colvars, 53
axis, 12 forceConstant, 53
forceNoPBC, 12 lambdaSchedule, 55
main, 12 name, 53
oneSiteTotalForce, 12, 13 outputAccumulatedWork, 56
ref2, 12 outputCenters, 54
ref, 12 outputEnergy, 53
distanceZ, dihedral, spinAngle, custom colvars targetCenters, 53
wrapAround, 26 targetEquilSteps, 55
distanceZ, custom colvars targetForceConstant, 55
period, 26 targetForceExponent, 55
distance targetNumStages, 54
forceNoPBC, 11 targetNumSteps, 54
group1, 11 writeTIPMF, 53
group2, 11 writeTISamples, 53
eigenvector histogramGrid
atoms, 21 lowerBoundaries, 61
differenceVector, 21 upperBoundaries, 61
refPositionsFile, 21 widths, 61
refPositions, 21 histogramRestraint
vectorFile, 21 colvars, 62
vector, 21 forceConstant, 62
gyration gaussianSigma, 62
atoms, 22 lowerBoundary, 62
hBond name, 61

66
 outputEnergy, 62 replicasRegistry, 51
refHistogramFile, 62 useGrids, 49
refHistogram, 62 wellTempered, 50
upperBoundary, 62 writeFreeEnergyFile, 49
width, 62 writeHillsTrajectory, 52
histogram writeHistogram, 62
colvars, 60 writeTIPMF, 48
gatherVectorColvars, 60 writeTISamples, 48
name, 60 orientationAngle
outputFileDX, 60 atoms, 23
outputFile, 60 refPositionsFile, 23
outputFreq, 60 refPositions, 23
weights, 60 orientationProj
inertiaZ atoms, 24
atoms, 22 refPositionsFile, 24
axis, 22 refPositions, 24
inertia orientation
atoms, 22 atoms, 23
linear closestToQuaternion, 23
centers, 58 refPositionsFile, 23
colvars, 58 refPositions, 23
forceConstant, 58 polarPhi
lambdaSchedule, 58 atoms, 16
name, 58 rmsd
outputAccumulatedWork, 58 atoms, 19
outputEnergy, 58 refPositionsFile, 20
targetEquilSteps, 58 refPositions, 20
targetForceConstant, 58 selfCoordNum
targetForceExponent, 58 cutoff3, 18
targetNumStages, 58 cutoff, 18
targetNumSteps, 58 expDenom, 18
writeTIPMF, 58 expNumer, 18
writeTISamples, 58 group1, 18
metadynamics pairListFrequency, 18
biasTemperature, 50 tolerance, 18
colvars, 48 spinAngle
dumpPartialFreeEnergyFile, 51 atoms, 24
hillWeight, 48 refPositionsFile, 24
hillWidth, 48 refPositions, 24
keepFreeEnergyFiles, 49 tilt
keepHills, 52 atoms, 25
multipleReplicas, 50 axis, 24, 25
name, 48, 52 refPositionsFile, 25
newHillFrequency, 48 refPositions, 25
outputEnergy, 48
rebinGrids, 50 any component
replicaID, 51 componentCoeff, 27
replicaUpdateFrequency, 51 componentExp, 27

67
 name, 25
scalable, 25
atom group
atomNumbersRange, 36
atomNumbers, 35
atomsOfGroup, 36
centerReference, 37
dummyAtom, 36
enableFitGradients, 38
enableForces, 38
fittingGroup, 38
indexGroup, 36
name, 35
refPositionsFile, 37
refPositions, 37
rotateReference, 37

colvar bias
colvars, 40
name, 40
outputEnergy, 40
writeTIPMF, 40
writeTISamples, 40

global
colvarsRestartFrequency, 6
colvarsTrajFrequency, 5
indexFile, 6
smp, 6

Keyword of the fix colvars command

input, 4
output, 4
seed, 4
tstat, 5
keyword of the fix colvars command
unwrap, 4

68
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