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Gromacs

General
Gromacs is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since Gromacs is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Policy
The Gromacs 3.2 program is available to users at NSC under the condition that published work include citation of the program (see below). Gromacs is Free Software , available under GNU General Public License .

Program citation
GROMACS: A package for molecular simulation and trajectory analysis, E. Lindahl and B. Hess and D. van der Spoel, J. Mol. Mod. 7 (2001) pp. 306-317

Manual
A manual is available. [here]

Essentials
In order to setup the Gromacs environment, execute the GMXRC shell script. The Gromacs binaries are thereby to be located in your path.

Running Gromacs will involve a number of input and output file types. An overview of the most important types is found [here]. In the example below, the following input file types are needed.

  • Initial molecular structure [.gro]
  • Topology file of water [.top]
  • Molecular Dynamics parameter file [.mdp]
  • Run input file [.tpr]

Gromacs on Monolith
In order to run an example with 216 water molecules in a box, copy the three input files conf.gro, topol.top, and grompp.mdp to your working directory

cp /usr/local/chem/gromacs-3.2/bin/share/tutor/water/* $HOME/calc/.
View the cluster structure (spc216.pdb) with for instance GView on Monolith.

Generate the run input file topol.tpr with the command

/usr/local/chem/gromacs-3.2/bin/linux/bin/grompp
The generated input file topol.tpr is the only file needed by the program mdrun in the MD simulation. To start the 20 picosecond MD simulation with use of 4 processors (2 nodes with 2 processors each) for one hour, submit the shell script below to the queue (the submit command is: qsub scriptname). The input files are assumed to be located in the directory $HOME/calc/
#!/bin/bash
#PBS -l walltime=1:00:00
#PBS -l nodes=2:ppn=2

. /usr/local/chem/gromacs-3.2/bin/linux/bin/GMXRC

WRKDIR=$HOME/calc/

cd $WRKDIR
grompp -np 4
mpprun /usr/local/chem/gromacs-3.2/bin/linux/bin/mdrun
After the calculaiton there are tools for visulization and analysis. Please, consult the manual for details on this particular example. [here]




Page last modified: 2004-06-01 20:51
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