BashScriptsForMassSimulations/test.sh at master · gmongell/BashScriptsForMassSimulations · GitHub

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#change the name of the folders
module load gromacs

cd /fs/lustre/cwr0408/
for l in EtOHMix50 EtOHMix00 EtOHMix70 EtOHMix100 EtOHMix80
do
cd /fs/lustre/cwr0408/$l
for dir in */
do
cd /fs/lustre/cwr0408/$l/$dir
echo $l
echo $dir
echo $l/$dir
echo $l\_${dir%?}\_density_${dir%?}\.xvg
echo $l\_${dir%?}\_density_EtOH.xvg
echo $l\_${dir%?}\_density_HOH.xvg
echo $l\_${dir%?}\_density_Sys.xvg
echo ${dir%/}
done
done


#doing it for one folder...it works

#change the name of the folders
module load gromacs
cd /fs/lustre/cwr0408/
for l in EtOHMix50
do
cd /fs/lustre/cwr0408/$l
for dir in */
do
cd /fs/lustre/cwr0408/$l/$dir
echo
echo -e "0\n1000\n9000\n" | trjcat -settime -f firstmd.trr secondmd.trr thirdmd.trr -o md_concat.trr
echo 0 | trjconv -f md_concat.trr -s $l\_${dir%?}\_EM.gro -o md_out.gro
echo $dir | ./AnalyzeGro4
echo -e "1" | g_density -f md_concat.trr -s md1.tpr -o $l\_${dir%?}\_density_${i%?}\.xvg -dens mass -d Z
echo -e "6" | g_density -f md_concat.trr -s md1.tpr -o $l\_${dir%?}\_density_EtOH.xvg -dens mass -d Z
echo -e "5" | g_density -f md_concat.trr -s md1.tpr -o $l\_${dir%?}\_density_HOH.xvg -dens mass -d Z
echo -e "0" | g_density -f md_concat.trr -s md1.tpr -o $l\_${dir%?}\_density_Sys.xvg -dens mass -d Z
done
done