#!/bin/csh -f 

set PDB = Na.pdb
set pdb_name = out.gro
set init_dist = 0.28
set A1 = NA1
set B1 = NA2
set boxlength = 4.0

#genera file inizio.pdb with 2 mol at begin c.o.m. distance

#editconf -f 2mer.pdb -bt cubic -box 4.0 -o inizio.pdb
editconf -f $PDB -box $boxlength -bt cubic -o $pdb_name
cat ndx | make_ndx -f $pdb_name -o index.ndx

cat > eq.mdp <<pluto
title               =  creol-wat MD
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  sd
ld_seed             = -1
tinit               =  0.0
dt                  =  0.002    
nsteps              =  800000    
nstcomm             =  1
nstxout             =  1000
nstvout             =  10000
nstfout             =  0
nstlog              =  1000
nstenergy           =  500
nstxtcout           =  500
nstlist             =  5
ns_type             =  grid
rlist               =  1.4
coulombtype         =  cut-off
rcoulomb            =  1.4
rvdw                =  1.4
pbc                 =  xyz
; Temperature coupling is on in two groups
Tcoupl              =  yes
tau_t               =  0.5        
tc-grps             =  system     
ref_t               =  300         
; Pressure coupling is  on
Pcoupl              =  no
ref_p               =  1.0
constraint-algorithm     = lincs
energygrps              = $A1 $B1
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull                     = constraint
pulldim = Y Y Y
pull_rate1 = 0.001 
pull_group_1 = $A1
pull_group_0 = $B1
pull_init1 = $init_dist
#
dihre                    = yes
dihre-fc                 = 1000
pluto

#cat > pull_ini.ppa <<pippo
#verbose = no
# runtype = constraint
# group_1 = $A1
# reference_group = $B1
# reftype = com
# reflag = 1
# Skip steps = 1
# pulldim = Y Y Y
# constraint_direction = 0.0 0.0 0.0
# constraint_rate1 = 0.001  
# constraint_distance1 = 0
# constraint_tolerance = 1E-6
#pippo

# new version version constraint_rate1 is pull_rate 
# standard version 3.3 
grompp -f eq.mdp -c $pdb_name -p topol.top -n index.ndx -o 
mdrun -v 


echo 0 | trjconv -f traj.trr -dt 20 -sep -o conf.gro -n index.ndx 
echo 1 2 | g_dist -f traj.xtc -n index.ndx -dt 20   
#grep -v "#" dist.xvg | grep -v "@" | awk '{printf "%10.1f %5.2f\n", $1, $2}'
grep -v "#" dist.xvg | grep -v "@" | awk '{printf "%10.0f %5.2f\n", $1/20, $2}' > file_dist.dat

mkdir confs
mv conf* ./confs/