#!/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

mkdir mindistnum_hydro_withoutca

#make index file
make_ndx -f system.pdb -o index_aa.ndx <<EOL
splitres 1
q
EOL

#loop over all residues

#calculate number of contacts between water and r14
#g_mindist -s system.pdb -f prod_time.xtc -n index_aa.ndx -od mindist.xvg -on polar_r14_SOL_group.xvg -tu us -d 0.3 -dt 0.1 -group -ox mindist.pdb <<EOL
#31
#16
#EOL

g_rdf -s system.pdb -f prod_time.xtc -n index_aa.ndx -cn rdf_r14-SOL_count.xvg -b 100000 <<EOL
31
16
EOL

#rm mindist.xvg