#! /usr/bin/perl -w

#  put the values of lambda that you want into the following array:
@clambda=( 0.00922, 0.04794, 0.11505, 0.20634, 0.31608, 0.43738, 0.56262, 0.68392, 0.79366, 0.88495, 0.95206, 0.99078 );

foreach $in ( 0 .. 12 ){ 

$out = $in + 1;

#    equilibration:

open( MDIN, ">mdin");

print MDIN <<EOF;
  diasppear valine 
 &cntrl
   ntr=0,
   nstlim =20000, nscm=2000, ntave=1000,
   ntx=1, irest=0, ntb=2, ntpr=100, tempi=300.0, ig=974651,
   ntp=1, taup=1.0,
   dt=0.001, nrespa=1,
   ntt=1, temp0 = 300., tautp=2.0,
   ntc=2, ntf=2, tol=0.000001, 
   ntwr = 1000, ntwx=0,
   icfe=1, clambda=${clambda[$in]}, klambda=6,
   cut=9.0,
 &end
EOF

close MDIN;

system("/theo1/tmp/amber8/exe/sander -O -i mdin  -p V93A-TI-FEP.top  -c eq$in.x  -o eq$out.out  -r eq$out.xe < /dev/null" );


#    production:


open( MDIN, ">mdin");

print MDIN <<EOF;
  diasppear valine
 &cntrl
   ntr=0,
   nstlim =100000, nscm=2000, ntave=1000,
   ntx=7, irest=1, ntb=1, ntpr=100, 
   ntp=0, taup=2.0,
   dt=0.001, nrespa=2,
   ntt=0, temp0 = 300., tautp=2.0,
   ntc=2, ntf=2, tol=0.000001, 
   ntwr = 1000, ntwx=0,
   icfe=1, clambda=${clambda[$in]}, klambda=6,
   cut=9.0,
 &end
EOF

close MDIN;

system("/theo1/tmp/amber8/exe/sander -O -i mdin  -p V93A-TI-FEP.top -c eq$out.xe  -o eq$out.o  -r eq$out.x < /dev/null" );

}