Gromacs

Program description:
A chemistry software package designed to simulate molecular dynamics. The program can be used for biochemical molecules (e.g. proteins, lipids) and non-biological systems (e.g. polymers).

Versions:

Name: Gromacs
Version: 4.6.3
Platform: x86_64
Category: Applications/Engineering
URL http://www.gromacs.org

Below is information on how to load the module into the software:
Module loading link

Sample SLURM startup script:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=28
#SBATCH --mem=15gb
#SBATCH -p standard
#SBATCH --time=30:00:00

# Set paths or load appropriate modules
module load gromacs/5.0.4

# Set the $TMPDIR variable
export TMPDIR=$HOME/grant_$SLURM_JOB_ACCOUNT/scratch/$USER/$SLURM_JOB_ID

# We set application variables
export SCR=${TMPDIR}

# We set auxiliary variables
INPUT_DIR="input"
OUTPUT_DIR="output"
OUTPUT_FILE="OUTPUT"

# Create a temporary directory
mkdir -p ${TMPDIR}

# Copy the input data to the directory pointed to by the $TMPDIR variable
cp ${SLURM_SUBMIT_DIR}/${INPUT_DIR}/* ${TMPDIR}

# Go to the $TMPDIR directory
cd $TMPDIR

# We do the calculations

grompp_mpi -f em.mdp -c box.gro -p topol.top -o topol_em.tpr
mdrun_mpi -v -s topol_em.tpr -c mixture150_em.gro
grompp_mpi -f grompp_LIQ_ich.mdp -c mixture150_em.gro -p topol.top -o topol_md_000_00.tpr -maxwarn 3

: the target job to be performed
mdrun_mpi -s topol_md_000_00.tpr -c mixture150_md_1.gro -o gro_b_1.trr -v



mpirun mdrun_mpi -deffnm topol_md_000_00.tpr -s topol_md_000_00.tpr -g topol_md_000_00.log -v> topol_md_000_00.out 2>&1

# Footer
cat << EOF
-------------------------------------------------- ---------------

End of calculations [$(date)].

-------------------------------------------------- ---------------
EOF

# We finish the calculations, copy the contents of the $TMPDIR/output directory
# to the directory from which the job was queued.
mkdir $SLURM_SUBMIT_DIR/${OUTPUT_DIR}
cp -r $TMPDIR/* $SLURM_SUBMIT_DIR/${OUTPUT_DIR}/

# Clear working directory
rm -rf $TMPDIR

Below are the files that should be in the input directory.
File:Gromacs input.zip