#!/bin/csh
#
set PDBID = "1AHO"

set BASEDIR = "/home/case/xtal/${PDBID}/"

cd ${BASEDIR}/

set IM = 17
@ I = $IM + 1

cat > md.in << EOF
Standard MD run input
 &cntrl

  nmropt = 0,
  ntx    = 5,       irest  = 1,
  ntrx   = 1,       ntxo   = 1,
  ntpr   = 10000,   ntwx   = 10000,  ntwr=100000,
  ntwv   = 0,       ntwe   = 10000,
  iwrap  = 0,       ioutfm = 1,

  ntf    = 2,       ntb    = 2,
  es_cutoff   = 12.0,
  vdw_cutoff  = 12.0,

  ibelly = 0,       ntr    = 0,

  imin   = 0,
  nstlim = 15000000,
  nscm   = 10000,
  t      = 0.0,     dt     = 0.002,

  temp0     = 293.0,   tempi  = 293.0,
  ig        = -1,
  ntt       = 3,
  gamma_ln  = 3.0,

  ntp    = 2,       pres0  = 1.0,     comp   = 44.6,
  taup   = 1.0,

  ntc    = 2,       tol    = 0.000001, watnam = 'WAT ',

 &end
 &ewald
  dsum_tol = 5.0e-6,
 &end
EOF


    # Run the MD simulation
/home/case/amber11/bin/pmemd.cuda -gpu 4 -O \
        -i md.in \
        -o md${I}.out \
        -p s${PDBID}.top \
        -c md${IM}.rst \
        -r md${I}.rst \
        -x md${I}.crd \
        -e md${I}.en \
        < /dev/null

