# do minimization

# author: mengen

#

# usage: ./modar step5_do_minimization.inp

#

#load force field

include "loadff.inc"

#load md system

loadmsf file="step4_all.msf"

#load PBC crystal setup

include "pbc.inc"

tell msf_info

#image groups

imggroup method=resid sorted=true select="resname tip* pot cl* sod"

#nonbond setup

nonbond type=pme nblcutoff=10.0 nbcutoff=8.0 swcutoff=7.0 eps=1.0 \

        beta=0.34 ftx=$fftx fty=$ffty ftz=$fftz bsorder=6

nstepminiall=200

echo -hs "|  running $nstepminiall steps minimization for whole system"

#do minimization for all

domin method=SDFuse nstep=$nstepminiall nprint=10 ftol=1e-5 fuse=0.2 \

      trjfile="mini.trj" frqtrj=10 \

      enefile="mini.ene" frqene=1

domin method=SD nstep=$nstepminiall nprint=10 ftol=1e-5 fuse=0.2 \

      trjfile="mini2.trj" frqtrj=10 \

      enefile="mini2.ene" frqene=1

#save msf and pdb

savemsf file="step5_minimized.msf"

savepdb fmt=pdb file="step5_minimized.pdb"

tell logfilename

echo -hs "|  output files:"

echo -hs "|    step5_minimized.mtf"

echo -hs "|    step5_minimized.pdb"

if(-var slogfn) {

  exec "grep minstep $slogfn | grep -v grep | awk '{print \$4}' > minipot.txt"

  echo -hs "|  please plot potential profile "minipot.txt" to check minimization result"

  echo -hs "|  for example: ./xmgr minipot.txt"

}

echo -hs "|  it's ready to go next step to heatup system by command:"

echo -hs "|    ./modar -nobak step6_heatup.inp"

echo -hs "| "