#!/bin/bash # # Code by venkentom@gmail.com # # Licenced by the GPL General Public License # Have a look at: # http://www.gnu.org/copyleft/gpl.html # For more information about the GPL License # # I am not responsible for what this code does to your hw/sw/mind # Use at your own risk # #Put gromacs commands after this line DIR=`pwd` #Config NPROCS=2 source /Home/ii/venken/.bashrc for i in {100..100} do mkdir $i cp system.top $i cp *.itp $i cp minimization.mdp $i cp assemble.mdp $i #has been set to 100 ns! cp genion.mdp $i cp submit* $i #has been set to 100 ns! genconf -f Tubby_CG.pdb -rot -o $i/genconf_${i}.gro j=$[ RANDOM % 9 ] k=$[ RANDOM % 9 ] l=$[ RANDOM % 9 ] cd $i editconf -f genconf_${i}.gro -o editconf.gro -box 9 9 9 -translate $j $k $l -noc genbox -cp editconf.gro -ci ../popc_single.gro -nmol 128 -try 500 -o genbox.gro grompp -f minimization.mdp -c genbox.gro -p ../system_noW.top -maxwarn 10 -o min-init.tpr mdrun -deffnm min-init -v genbox -cp min-init.gro -cs ../polarize-water.gro -o waterbox.gro -maxsol 1500 -vdwd 0.21 grompp -f genion.mdp -c waterbox.gro -p system.top -o system_neutral.tpr genion -s system_neutral.tpr -o system_neutral.gro -p system.top -pname NA+ -nname CL- -neutral -conc 0.000001 << EOL PW EOL make_ndx -f system_neutral.gro -o index.ndx <