GROMACS

Policy

GROMACS is available to users at HPC2N under the condition that published work include citation of the program. GROMACS is Free Software, available under the GNU General Public License.

General

GROMACS (GROningen MAchine for Chemical Simulations) is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

Description

GROMACS was first developed in Herman Berendsens group, department of Biophysical Chemistry of Groningen University. It is a team effort, with contributions from several current and former developers all over world.

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, lipids and nucleic acids 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.

GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation.

Availability

On HPC2N we have GROMACS available as a module on Akka and Abisko.

Usage at HPC2N

To use the gromacs module, add it to your environment:

module add gromacs

There are several versions. To use a different one than the default, run module avail and look for gromacs for the versions available.

Loading the module should set all the needed environmental variables as well as the path. 

To run Gromacs, you first need to prepare various input files (conf.gro for coordinates, topol.top for topology and the main parameters file, grompp.mdp). Then you should run the preprocessor grompp, followed by the main energy minimization program mdrun. It is possible to extend the simulation with subsequent mdrun steps, and perhaps use tpbconv to prepare the input from the files generated from a previously terminated run. When you are using a parallel version of mdrun, it is important that the number of processors used for mdrun is the same as the number specified in the grompp step.

A few options for grompp (type grompp without anything else for a list with more):

Option     Filename  Type         Description
------------------------------------------------------------
  -f     grompp.mdp  Input, Opt.  grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c       conf.gro  Input        Structure file: gro g96 pdb tpr tpb tpa
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
 -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n      index.ndx  Input, Opt.  Index file
  -p      topol.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o      topol.tpr  Output       Run input file: tpr tpb tpa
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e       ener.edr  Input, Opt.  Energy file: edr ene

Some options for mdrun (type mdrun without anything elase for a list with more):

Option     Filename  Type         Description
------------------------------------------------------------
  -s      topol.tpr  Input        Run input file: tpr tpb tpa
  -o       traj.trr  Output       Full precision trajectory: trr trj cpt
  -x       traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi      state.cpt  Input, Opt.  Checkpoint file
-cpo      state.cpt  Output, Opt. Checkpoint file
  -c    confout.gro  Output       Structure file: gro g96 pdb
  -e       ener.edr  Output       Energy file: edr ene
  -g         md.log  Output       Log file
-dgdl      dgdl.xvg  Output, Opt. xvgr/xmgr file
-field    field.xvg  Output, Opt. xvgr/xmgr file
-table    table.xvg  Input, Opt.  xvgr/xmgr file
-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
-tableb   table.xvg  Input, Opt.  xvgr/xmgr file
-rerun    rerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpi        tpi.xvg  Output, Opt. xvgr/xmgr file
-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
 -ei        sam.edi  Input, Opt.  ED sampling input
 -eo        sam.edo  Output, Opt. ED sampling output
  -j       wham.gct  Input, Opt.  General coupling stuff
 -jo        bam.gct  Output, Opt. General coupling stuff
-ffout      gct.xvg  Output, Opt. xvgr/xmgr file
-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
-runav  runaver.xvg  Output, Opt. xvgr/xmgr file
 -px      pullx.xvg  Output, Opt. xvgr/xmgr file
 -pf      pullf.xvg  Output, Opt. xvgr/xmgr file
-mtx         nm.mtx  Output, Opt. Hessian matrix
 -dn     dipole.ndx  Output, Opt. Index file

Example, Akka

Below is an example how to run a serial Gromacs job on Akka. Note that you must run from the parallel file system.

#!/bin/bash
#PBS -o gromacs.out
#PBS -j y
# Change the account below to a valid project account 
#PBS -A SNICXXX-YY-Z
#PBS -N gromacs
#PBS -l nodes=1
#PBS -l walltime=1:00:00

module add gromacs

# Assume that the job file are located in the submit directory
cd $PBS_O_WORKDIR

grompp -f input.mdp -p topol.top -c conf.gro -o topol.tpr
mdrun -s topol.tpr -o traj.trr -c confout.gro -g md.log

#
# End of script
#            

Submit the script with qsub <scriptname>. More information about batchscripts here.

Example, Abisko

Below is an example how to run a serial Gromacs job on Abisko. Note that you must run from the parallel file system.

#!/bin/bash
# Change to your actual SNIC project number
#SBATCH -A SNICXXX-YY-ZZ
# Asking for one node and all cores on it
#SBATCH -N 1
#SBATCH --exclusive
# Asking for 30 hours walltime
#SBATCH -t 30:00:00
# Names the error and output files according to the jobid
#SBATCH --error=gromacs_%J.err
#SBATCH --output=gromacs_%J.out
#SBATCH --mail-type=ALL

# Loads the module gromacs. This can also be
# done before submitting the job, as the environment is exported
module add gromacs

# Getting some information about the nodes
echo $SLURM_JOB_NODELIST
echo 'node:    ' $HOSTNAME

grompp -f input.mdp -p topol.top -c conf.gro -o topol.tpr
srun mdrun_mpi -s topol.tpr -o traj.trr -c confout.gro      

Submit the script with sbatch <scriptname>. More information about batchscripts here.

Additional info

Documentation is available on the Gromacs documentation page and the Gromacs Online Reference page.