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Terminologies MD Process Analysis of Trajectories Short Practical Session

This document outlines the process of performing a molecular dynamics simulation using GROMACS. It discusses key terminologies like force fields and topology. It describes preparing the system by setting up input files, solvating, minimizing energy, and equilibrating temperature and pressure. The document concludes by discussing running the actual MD production and analyzing the resulting trajectories.

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Musyoka Thommas Mutemi
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107 views14 pages

Terminologies MD Process Analysis of Trajectories Short Practical Session

This document outlines the process of performing a molecular dynamics simulation using GROMACS. It discusses key terminologies like force fields and topology. It describes preparing the system by setting up input files, solvating, minimizing energy, and equilibrating temperature and pressure. The document concludes by discussing running the actual MD production and analyzing the resulting trajectories.

Uploaded by

Musyoka Thommas Mutemi
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPTX, PDF, TXT or read online on Scribd
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Outline

Introduction

Terminologies

MD process

Analysis of trajectories

Short Practical session


Introduction

Integrate Newtons 2nd law of motion for all atoms in a system

GROningen MAchine for Chemical Simulations

A versatile engine md simulations and energy minimization

Suited for biochemical molecules lipids, proteins, nucleic acids, polym

Outcome of an MD process
Molecular interactions
Terminologies

Force field form & parameters of mathematical functions used to desc


All-atom
United-atom
Coarse-grained
Energy minimization non dynamical calculation of local potential ener
Steepest descent
Conjugate gradient
L-BFGS
Topology Complete descriptions of all atomic interactions in a system
Terminologies (cont)

Equilibration solvent relaxation


NVT - canonical
NPT - isothermal-isobaric
NVE - microcanonical
Blowing up simulation failure
Inadequate minimization
Bad structure
Too large time step
Inappropriate pressure/temperature coupling
Files

Input files
*.pdb Protein data bank (atom coordinates)
*.gro Gromacs format (atom coordinates + velocities)
*.itp atom information (charges, mass, radii)
*.top topology file
*.mdp MD simulation parameters
*.tpr run input file (all information for an MD run)
*.ndx index file {control operations (specify groups)}
Output files
*.trr trajectory (atom coordinates + velocities)
*xtc trajectory filr (atom co-ordinates ONLY)
*.edr trajectory file (energies)
Log CPU time, restart runs
Scripts

Ionization (ion.mdp)

Energy minimization (em.mdp)

Temparature coupling (nvt.mdp)

Pressure coupling (npt.mdp)

MD real run (md.mdp)


Ion & energy minimization script
Nvt & npt ensemble script
Md run script
Methodology Pre-MD

Starting structures
A protein PDB, Ligand PDB
Pre-MD process
Cleaning structures
Ligand topology external tools (PRODRG, ATP builder, ACPYPE)
Most challenging force fields cant handle foreign species (parametize)
Derive & validate force field parameters
Pdb-gromacs conversion
Use pdb2gmx top, itp and posres
Define pbc & solvate
Use editconf boxed.gro
Use genbox solvated_boxed.gro
Ionise Use genion ionised_solvated_boxed.gro
Energy minimization & equilbration

Input files ionised_solvated_boxed.gro + topology

Energy minimization
Use grompp and mdrun em.gro

Temperature coupling
Use grompp and mdrun nvt.gro

Pressure coupling
Use grompp and mdrun npt.gro
Final MD run & analysis

Input files npt.gro and topology

Production of a final md.tpr and mdrun


Use grompp
Mdrun md.tpr, md.trr, md.xtc, md.edr

Analysis First view trajectories


g_rms
g_rmsf
g_gyrate
References

http://www.gromacs.org/
http://en.wikipedia.org/wiki/GROMACS
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
http://md.chem.rug.nl/cgmartini/index.php/proteins
http://www.swissparam.ch/SwissParam_gromacs_tutorial.html
http://compbio.biosci.uq.edu.au/education/mdcourse/Analysis.html
http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water
http://www.biocode.it/tutorial-mds-5.php

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