# equilibration using Nose-Hoover thermostat

# author: mengen

#

# usage: ./modar step7_equil.inp -o step7.log nstep=5000

#        nstep default is 5000

#

if(! -var nstep) {

  nstep=5000

  echo -hs " no nstep specified"

  echo -hs "   $nstep steps will be"

  echo -hsn "   or tell it now:"

  n=gettext()

  if($n>1000 && $n<100000) nstep=$n

}

#load force field

include "loadff.inc"

#load md system with minimized state

loadmsf file="step6_heatup.msf"

tell msf_info

loadmdc file="step6_heatup.mds"

#change to nosehoover thermostat

ensemble nvt tcoup=nosehoover

#or change to langevin thermostat

#ensemble nvt tcoup=langevin

mdcp trjfile="step7_equil_nvt.trj" frqtrj=100 \

     enefile="step7_equil_nvt.ene" frqene=100 \

     rstfile="step7_equil_nvt.rst" frqrst=20000 \

     nstepmore=$nstep nprint=100

savesetup file="step7_equil_nvt.mds"

echo -hs " running $nstep NVT equilibration ..."

runmd

savecrd fmt=pdb file="step7_equil_nvt.pdb"

echo -hs "|  output files:"

echo -hs "|    step7_equil_nvt.mds"

echo -hs "|    step7_equil_nvt.rst"

echo -hs "|    step7_equil_nvt.trj"

echo -hs "|    step7_equil_nvt.ene"

echo -hs "|    step6_equil_nvt.pdb"

echo -hs "| "

echo -hs "|  it's ready to go next step to do a short NPT equilibration"

echo -hs "|    ./modar step8_equil_npt.inp nstep=5000"

echo -hs "| "