#!/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

# !! to switch to semiisotropic pressure coupling, make sure membrane is aligned to the x-y plane !!

editconf -f assemble_100.pdb -rotate 0 90 0 -noc -o system.gro <<EOL
0
EOL

grompp -f equilibration.mdp -c system.gro -p system.top -o equilibration.tpr 
mdrun -deffnm equilibration -v -nt 4

#grompp -f dynamic.mdp -c equilibration.gro -p system.top -o dynamic.tpr  -t equilibration.trr
#mdrun -deffnm dynamic -v -nt 4


rm \#*