BashScriptsForMassSimulations/testingmodulecall.pbs at master · gmongell/BashScriptsForMassSimulations · GitHub

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#PBS -N PE_10C_MS8ns
#PBS -j oe
#PBS -m abe
#PBS -M gfm12@case.edu
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=12
#PBS -S /bin/bash
set -vx

#Alcohol name variable
X=Et
echo "$XOH"
#Alcohol content variable
C=80
echo "$C%"
#Core Folder
Fold=/fs/lustre/cwr0408/1.29.2014/
echo "$Fold"
#load the gromacs modules
module load gromacs/4.6.3

i=PP18
cd /fs/lustre/cwr0408/1.29.2014/$i
#a place to put all of the derived outputs
mkdir ./outputs
cd /fs/lustre/cwr0408/1.29.2014/$i
#need to correct PE4 to have 3 pbs scripts
#making the ndx file for hoh ordering (only includes waters)
echo -e "name Water\nq" | make_ndx -f md_out.gro -o index.ndx
#making the gro file for the calculation of the order parameter
#echo 1 | trjconv -f md_concat.trr -s EtOHMix80_PP18_EM.gro -o md_out_order.gro
#may need to create a special gro file with only water molecules (ndx required)
#echo 1 | g_order -f md_out_order.gro -s md1.tpr -o order.xvg

#multiple rdf and density calls should be performed ( density for each species [3] and mixture; rdf for each solvent [2])
#computing the rdf of the polymer with water, then alcohol (no ndx needed)
echo -e "6\n1" | g_rdf -f md_concat.trr -s md1.tpr -o $XOH$C_$i_rdf_HOH.xvg -com
echo -e "6\n5" | g_rdf -f md_concat.trr -s md1.tpr -o $XOH$C_$i_rdf_$COH.xvg -com
echo -e "1" | g_density -f md_concat.trr -s md1.tpr -o $XOH$C_$i_density_$i.xvg -dens mass -symm -d Z
echo -e "6" | g_density -f md_concat.trr -s md1.tpr -o $XOH$C_$i_density_$COH.xvg -dens mass -symm -d Z
echo -e "5" | g_density -f md_concat.trr -s md1.tpr -o $XOH$C_$i_density_HOH.xvg -dens mass -symm -d Z
echo -e "0" | g_density -f md_concat.trr -s md1.tpr -o $XOH$C_$i_density_Sys.xvg -dens mass -symm -d Z
#still need to plot and derive kD, althogh it is given as a runtime output in the log
#no ndx required for msd computations
echo 6 | g_msd -f md_concat.trr -s md1.tpr -o msd.xvg
echo 6 | g_gyrate -f md_concat.trr -s md1.tpr -o $XOC$C_$i_gyrate.xvg
#since the .edr files are not concatenatable, this is performed in three steps
#for plotting together in excel
echo 2 3 4 5 6 7 8 12 33 34 35 36 23 27 31\n | g_energy -f firstmd.edr -s md1.tpr -o $XOH$C_$i_energy1.xvg
echo 2 3 4 5 6 7 8 12 33 34 35 36 23 27 31\n | g_energy -f secondmd.edr -s md2.tpr -o $XOH$C_$i_energy2.xvg
echo 2 3 4 5 6 7 8 12 33 34 35 36 23 27 31\n | g_energy -f thirdmd.edr -s md3.tpr -o $XOH$C_$i_energy3.xvg