evaluate.gromacs

name=$1

# add all ions
awk '{
  ions[1]="CL"
  ions[2]="NA"
  ions[3]="K "
  ions[4]="RB"
  ions[5]="CS"
  ions[6]="LI"
  if($3=="NA" || $3=="CL"){
      c=c%6
      c++
      print substr($0,1,13)""ions[c]"   "ions[c]""substr($0,21)
  } else print
}' $name > gromacs.pdb

# delete gromacs backups
rm -fr \#*

# setup with infinite cutoff
cat > grompp.mdp << EOF
integrator  = md
nsteps	    = 1
nstlist	    = 1	
ns_type	    = simple
coulombtype = cut-off
rlist       = 0.0
rcoulomb    = 0.0
rvdw  	    = 0.0
pbc         = no
EOF

# adjust this depending on your gromacs suffix
suffix=_mpi_d

rm -f topol.tpr conf.gro energy.xvg out err

{
# use first force field available
echo 1
echo 6
} | pdb2gmx$suffix -f gromacs.pdb  >> out 2>> err

grompp$suffix  >> out 2>> err && mdrun$suffix -rerun conf.gro  >> out 2>> err && {
  echo 1 2 3 4 5 6 7 8
} | g_energy$suffix -f ener.edr -xvg none  >> out 2>> err

awk '{
#  printf("Bond str    angles      dihedral       LJ-14        coulomb-14   LJ          coulomb       total\n");
  printf("%11f %11f %11f %11f %11f %11f %11f\n",$2,$3,$4+$5,$6,$7,$8,$9);
}' energy.xvg