ICHEC Software
Information about software packages installed on the ICHEC systems.
GROMACS
Versions Installed
Stokes: 4.5.1
Description
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 as GROMACS is fast at calculating the nonbonded interactions there is also much research on non-biological systems, e.g. polymers.
License
GROMACS is available under the GNU General Public License.
Benchmarks
N/A.
Job Submission Example
#!/bin/bash
#PBS -N MyJobName
#PBS -j oe
#PBS -r n
#PBS -A MyProjectCode
#PBS -l nodes=1:ppn=12
#PBS -l walltime=00:10:00
module load gromacs
cd $PBS_O_WORKDIR
# pre-process the input for start
# grompp_d -f grompp.mdp -p topol.top -c conf.gro -o water.tpr
grompp_d MyOptions and Files
# start the md
# mpiexec mdrun_d -s water.tpr -o water.trr -c water.out -g water.log
mpiexec mdrun_d MyOptions and files
#PBS -N MyJobName
#PBS -j oe
#PBS -r n
#PBS -A MyProjectCode
#PBS -l nodes=1:ppn=12
#PBS -l walltime=00:10:00
module load gromacs
cd $PBS_O_WORKDIR
# pre-process the input for start
# grompp_d -f grompp.mdp -p topol.top -c conf.gro -o water.tpr
grompp_d MyOptions and Files
# start the md
# mpiexec mdrun_d -s water.tpr -o water.trr -c water.out -g water.log
mpiexec mdrun_d MyOptions and files
Additional Notes
Further information can be obtained at www.gromacs.org.