GROMACS

Versions Installed

Kay: 2018.3

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

To run the code in parallel on Kay, please follow the below example. 

#!/bin/sh
# All the information about queues can be obtained using 'sinfo'
# PARTITION AVAIL  TIMELIMIT  
# DevQ         up    1:00:00   
# ProdQ*       up 3-00:00:00    
# LongQ        up 6-00:00:00    
# ShmemQ       up 3-00:00:00    
# PhiQ         up 1-00:00:00   
# GpuQ         up 2-00:00:00    

# Slurm flags
#SBATCH -p ProdQ
#SBATCH -N 2
#SBATCH -t 02:00:00
#SBATCH --job-name=gromacsjob

# Charge job to myproject 
#SBATCH -A myproject

# Write stdout+stderr to file
#SBATCH -o output.txt

# Mail me on job start & end
#SBATCH --mail-user=my@email.ie
#SBATCH --mail-type=BEGIN,END

cd $SLURM_SUBMIT_DIR

module load gromacs/2018.3

mpirun -np 80 gmx_mpi_d mdrun -deffnm prod

Additional Notes

Further information can be obtained at www.gromacs.org.