Gromacs

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Last Modified: 07/30 14:39

Description

From the Gromacs manual: GROMACS is an engine to perform molecular dynamics simulations and energy minimization.

Version

• 3.3.3

Authorized Users

• circe account holders

Platforms

• circe cluster

Local Documentation

Modules

Gromacs requires the following module file and some prerequisites to run:

• apps/gromacs/3.3.3
• Prerequisites: compilers/intel/10.1.008.x86_64 openmpi/1.2.6-x86_64-intel-10.1.008

To run Gromacs on the cluster, ensure that you use module initadd to make the changes persistent. See Modules for more information.

Submitting Jobs

First, you will need a protein or molecule to play with. Go to  http://www.rcsb.org/pdb/ and grab one in .pdb format.

This is the procedure for simple molecules.

• Run pdb2gmx_d -f <pdb file> on it to convert it to a .gro file and a (possible series of) .top file(s).

• Run editconf_d with proper parameters to change the dimensions of the box.

• Run genbox_d with proper parameters to add solvate.

• Run grompp_d and mdrun_d in an sge script to perform the simulation. A sample sge script is provided below. For more information on submit scripts, see GridEngine Submit Techniques:

  #!/bin/bash
  #$ -N gromacs_test
  #$ -cwd
  #$ -pe ompi* 4
  #$ -o output.$JOB_ID
  #$ -j y
  #$ -q amd64.q
  #$ -l h_rt=8:00:00
  
  grompp_d -np $NSLOTS
  sge_mpirun /opt/apps/gromacs-3.3.3/bin/mdrun_d
  

The _d appended to each binary stands for the double-precision version of the binary. It is not recommended to run single- and double-precision binaries interchangeably for the same simulation.

An additional file is needed for grompp_d called grommp.mdp. You can grab a copy of it from /usr/local/apps/gromacs/share/gromacs/tutor/methanol and modify it in your local directory as needed.