#!/bin/csh -f

#PBS -l nodes=2:ppn=4
#PBS -l walltime=12:00:00
#PBS -l cput=12:00:00
#PBS -m ae
##PBS -M jana.k.shen@ou.edu

# set shell variables (job name, running, working directories, etc)
set ncpu = 8
set nreplica = $ncpu
set ph = 4
set pdb = cpept
set jobname = rex-${pdb}.ph-$ph
set struct = ${pdb}_h
set workdir = ~/cphmd
set rundir = $PBSREMOTEDIR/$jobname
set rexdir = ${pdb}.ph-$ph
set nstep = 500

mkdir $rundir

# copy input files from $workdir to $rundir
cd $rundir
cp $workdir/struct/${struct}.pdb init.pdb
cp $workdir/struct/${struct}.crd init.crd
cp $workdir/struct/${struct}.psf init.psf
sed 's/gbsw sgamma 0.005 nang 50/gbsw sgamma 0.005 nang 50 conc 0.15/' $workdir/toppar/setup-gbsw.str > setup.str

# create a file "hostlist", which contains info about compute nodes for replica-exchange simulation
cat $PBS_NODEFILE | sort -u | awk ' { print $1, " 4 ",dir } ' dir=$PBSTMPDIR > hostlist

# run replica-exchange simulation for 500 steps
aarex.pl -mp -hosts hostlist -n ${nstep} -charmmlog logfile -par archive,psf=init.psf,natpdb=init.pdb  -temp ${nreplica}:298:400 -dir ${rexdir} -mdpar param=22x,xpar=par_all22_prot_cmap_phmd.inp,xtop=top_all22_prot_cmap_phmd.inp,lang,langfbeta=5.0,dynoutfrq=500,dyntrfrq=500,dynsteps=500,gb=gbsw,gbswsgamma=0.005,scalerad=nina,cutnb=24.0,cutoff=20.0,cuton=20.0,phmdpar=phmd.in,phmdpri=500,phmdph=${ph} -custom setup setup.str init.crd

exit