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.

GROMACS is licensed and redistributed under the GPL.

Please consult the GROMACS web site for further information on this package.

The xdrfile library facility for I/O to xtc, edr and trr files is also available.

Pour voir les versions installées :

$ module avail gromacs
 gromacs/mpi/gcc/2016    gromacs/mpi/gcc/2016-sp gromacs/mpi/gcc/2018-sp gromacs/mpi/gcc/5.1.2

gromacs.sge

#!/bin/bash -l
 
#$ -o $JOB_NAME.o$JOB_ID
#$ -N gromacs
#$ -q parallel.q
 
## we request 32 cores
#$ -pe mpi 32  
 
### we use version 2018 for example :
module load gromacs/mpi/gcc/5.1.2
 
mpirun -np $NSLOTS gmx_mpi mdrun_mpi -s test.tpr

Submit your script:

$ qsub gromacs.sge