GROMACS

Introduction

GROMACS is a package for molecular dynamics simulation and energy minimization.

In GROMACS,

  • the simulations are classical, using Newton's equation of motion;
  • electrons are in the ground state. Electronic motions are not considered;
  • force fields are approximate;
  • the force field is pair-additive;
  • long range interactions are cut off;
  • boundary conditions are unnatural (periodic);

GROMACS can be run in parallel, on any system which includes the MPI library.

The project site is http://www.gromacs.org.

Documentation is available in:

Availability

The most recent version of GROMACS on Cascades is 2016.a. On BlueRidge, DragonsTooth, HokieSpeed, and NewRiver, the most recent version is 5.12. HokieOne's most recent version is 4.55.

To see all the versions of GROMACS available on a particular ARC given cluster, type:

      module spider gromacs

To use GROMACS on an ARC cluster, it is necessary to issue the appropriate module commands. To make version 5.0.5 available on NewRiver, the appropriate commands would be:

      module purge
      module load intel/15.3
      module load openmpi/1.8.5
      module load mkl/11.2.3
      module load gromacs/5.0.5

After issuing these commands, the GROMACS executable is available as gmx. A typical invocation of gmx will be followed by a keyword that identifies the specific operation to be carried out, followed by several switches and parameters. For example, the editconf function can set the size of the box surrounding the data, and might be invoked by a command like:

      gmx editconf -f 1aki_processed.gro -o 1aki_newbox.gro -c -d 1.0 -bt cubic

Some GROMACS commands, such as for plotting, expect user interaction. If these commands are to be given as part of a batch file, then the user must supply the commands as input files. For instance, the GROMACS energy keyword analyzes the energy terms, but needs the user to select which energy function to analyze. To execute this in batch mode, the user might enter the appropriate numerical index in a text file energy_choice.txt, so that the full command would be:

      gmx energy -f em.edr -o potential.xvg < energy_choice.txt

Examples

Here is an example of a batch file that could be used to run GROMACS on the ARC NewRiver cluster. Note that this example only carries out the first few commands of an extensive analysis described in Justin Lemkul's website referenced above. The full analysis is presented in the tar file.

#! /bin/bash
#
#PBS -l walltime=00:45:00
#PBS -l nodes=1:ppn=24
#PBS -W group_list=newriver
#PBS -q open_q
#PBS -j oe

cd $PBS_O_WORKDIR

module purge
module load intel/15.3
module load openmpi/1.8.5
module load mkl/11.2.3
module load gromacs/5.0.5
#
#  Read the PDB file, generate topology, restraint, and structure files.
#
gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce < pdb2gmx_input.txt
#
#  Define the box dimensions.
#
gmx editconf -f 1aki_processed.gro -o 1aki_newbox.gro -c -d 1.0 -bt cubic
#
#  Fill the box with water.
#
gmx solvate -cp 1aki_newbox.gro -cs spc216.gro -o 1aki_solv.gro -p topol.top

A complete set of input files and a batch script for Justin Lemkul's 1AKI tutorial example are available in this tar file.