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GROMACS

GROMACS is a highly optimized open source molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids that have a lot of complicated bonded interactions. Gromacs 5.0.4 is compiled and installed in the HPC cluster using different compilers and different levels of acceleration.

Please use the following template to create your submission script to submit your molecular dynamics simulation jobs to the parallel LSF batch queues:

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#!/bin/bash
#PBS -P Proj_gromacs
#PBS -j oe
#PBS -N my_gromacs_job
#PBS -q parallel12     ###or: parallel24
#PBS -l select=2:ncpus=12:mpiprocs=12:mem=20GB        ### for parallel24: ncpus=24:mpiprocs=24
cd $PBS_O_WORKDIR;
export OMP_NUM_THREADS=12
np=$(cat ${PBS_NODEFILE} |wc -l);
source /etc/profile.d/rec_modules.sh
module load gromacs511_gmp           ### or: load gromacs514_im 
jname=md
mpirun -f ${PBS_NODEFILE} -np $np mdrun_mpi -ntomp ${OMP_NUM_THREADS} -pin on -nice 0 -v -s $jname.tpr -o $jname.trr -cpo $jname.cpt -c $jname.gro -e $jname.edr -g $jname.log –x $jname.xtc
#!/bin/bash
#PBS -P Proj_gromacs 
#PBS -j oe
#PBS -N 

#PBS -q parallel24  ## or, parallel 12
#PBS -l select=1:ncpus=24:mpiprocs=24:mem=20GB
cd $PBS_O_WORKDIR;
export OMP_NUM_THREADS=12
np=$(cat ${PBS_NODEFILE} |wc -l);
source /etc/profile.d/rec_modules.sh
module load gromacs514_im
jname=md
gmx mdrun -ntomp ${OMP_NUM_THREADS} -pin on -nice 0 -v -s $jname.tpr -o $jname.trr -cpo $jname.cpt -c $jname.gro -e $jname.edr -g $jname.log -x $jname.xtc

Using the following script to submit jobs with Gromacs GPU version to the gpu queue:

#!/bin/sh
#PBS -P Proj_Gromacs_GPU
#PBS -j oe
#PBS -N my_gpu_job
#PBS -q gpu
#PBS -l select=3:ncpus=12:mpiprocs=2:mem=20GB
cd $PBS_O_WORKDIR;
export OMP_NUM_THREADS=6
source /etc/profile.d/rec_modules.sh
module load gromacs511_gmp
np=$(cat ${PBS_NODEFILE} |wc -l);
jname=md

mpirun -f ${PBS_NODEFILE} -np $np mdrun_mpi -resethway -noconfout -ntomp ${OMP_NUM_THREADS} -pin on -gpu_id 01 -nb auto -nice 0 -v -s $jname.tpr -o $jname.trr -cpo $jname.cpt -c $jname.gro -e $jname.edr -g $jname.log -x $jname.xtc
$qsub run_script

Please use the high performance parallel file system /hpctmp2 or /hpctmp as your working directory.

Apart from submitting molecular dynamics simulation job to the parallel batch queues, you can also run many other Gromacs Programs interactively at the command prompt, i.e.:

$ gmx pdb2gmx -f dna.pdb -o dna.gro

Type “gmx command –h” to get usage help, or refer to the following web pages for more details:
http://manual.gromacs.org/programs/bytopic.html

http://manual.gromacs.org/documentation/

Please email nusit-hpc@nus.edu.sg for any problems or queries.