add scripts to run gromacs gpu

Author: mariojmdavid

udocker-files/gromacs-gpu/run-grom-gpu.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+. /usr/local/gromacs/bin/GMXRC.bash
+
+gmx mdrun -s /home/user/input/md.tpr -e $EDR -x $XTC -o $TRR -g $LOG \
+    -maxh 0.50 -resethway -noconfout -nsteps 10000 -nt 8 -pin on

udocker-files/run-gromacs-gpu.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+#SBATCH --job-name=run_gromacs_gpu
+#SBATCH --ntasks=8
+#SBATCH --partition=gpu
+#SBATCH --output=gromacs-gpu-%j.out
+#SBATCH --error=gromacs-gpu-%j.err
+
+export TUT_DIR=$HOME/udocker-tutorial
+export PATH=$HOME/udocker-1.3.17/udocker:$PATH
+export UDOCKER_DIR=$TUT_DIR/.udocker
+export GROM_INPUT=$TUT_DIR/udocker-files/gromacs-gpu
+
+export OUT_NAME=$GROM_INPUT/output/ud-gpu-tutorial
+export TRR=${OUT_NAME}.trr
+export XTC=${OUT_NAME}.xtc
+export EDR=${OUT_NAME}.edr
+export LOG=${OUT_NAME}.log
+mkdir -p $OUT_NAME
+module load python
+cd $TUT_DIR
+
+echo "###############################"
+udocker run -v=$GROM_INPUT:/home/user -w=/home/user grom_gpu /home/user/run-grom-gpu.sh