#!/bin/csh -f

set lambda = 0.5

cat > mdin_min1 <<EOF
Initial Minimization of solvent + ions
 &cntrl
  imin   = 1,
  maxcyc = 1000,
  ncyc   = 500,
  ntb    = 1,
  ntr    = 1,
  cut    = 10.0,
  icfe = 2, klambda = 6, clambda = $lambda
 /
Hold the RNA fixed
500.0
RES 1 8
END
END
EOF

cat > mdin_min2 <<EOF
Initial Minimization of the whole system
 &cntrl
  imin   = 1,
  maxcyc = 2500,
  ncyc   = 1000,
  ntb    = 1,
  ntr    = 0,
  cut    = 10.0,
  icfe = 2, klambda = 6, clambda = $lambda
 /
EOF

cat > groups1 <<EOF
-O -i mdin_min1 -p ../ggcc.prmtop     -c ../ggcc.inpcrd -o min1_out.$lambda.p1 -r min1.p1.rst -ref ../ggcc.inpcrd
-O -i mdin_min1 -p ../igigicic.prmtop -c ../ggcc.inpcrd -o min1_out.$lambda.p2 -r min1.p2.rst -ref ../ggcc.inpcrd
EOF

cat > groups2 <<EOF
-O -i mdin_min2 -p ../ggcc.prmtop     -c min1.p1.rst -o min2_out.$lambda.p1 -r min2.p1.rst 
-O -i mdin_min2 -p ../igigicic.prmtop -c min1.p2.rst -o min2_out.$lambda.p2 -r min2.p2.rst 
EOF

mpi 4 ~/amber9/exe/sander.MPI -ng 2 -groupfile groups1 < /dev/null || goto error
mpi 4 ~/amber9/exe/sander.MPI -ng 2 -groupfile groups2 < /dev/null || goto error

/bin/rm mdin_min1 mdin_min2 groups1 groups2

exit(0)
echo "  ${0}:  Program error"
exit(1)
