if(! -var nstep) getvar nstep default=5000 min=1000 msg="How may steps to run"

#load force field

include "loadff.inc"

#load MSF built previously

loadmsf file="step5_largebox.msf"

#load pbc setup

include "pbc.inc"

#image groups

imggroup method=resid sorted=true select="all"

#constraint

shake type=bondH tol=1e-6 scale=1.0 maxite=500 ref=para

#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

#heat up using Berendsen thermostating

ensemble NVT tcoup=Berendsen ttcoup=2.0 Tinit=50 Tref=300

#build MD core

build mdcore  timestep=0.002 nprint=100 \

     trjfile="step6_heatup.dcd" frqtrj=100 trjfmt=charmm \

     enefile="step6_heatup.ene" frqene=10 \

     rstfile="step6_heatup.rst" frqrst=100000 \

     flushene=true \

     randseed=314159 randtype=old \

     frqresort=20000

#run MD

runmd nstepmore=$nstep

#change to Nose-Hoover thermostat

ensemble tcoup=nosehoover tmass=1000

#change output files name

mdcp trjfile="step6_equil_nvt.trj" frqtrj=250 trjfmt=movar \

     enefile="step6_equil_nvt.ene" frqene=10 \

     rstfile="step6_equil_nvt.rst" \

     resetstartstep=true

#save mds for restarting run

savemdcore file="step6_equil_nvt.mds"

#run MD

runmd nstepmore=$nstep