AMBER Archive (2004)

Subject: Re: AMBER: Free energy in Amber8

From: David A. Case (case_at_scripps.edu)
Date: Tue Jun 01 2004 - 14:17:34 CDT

On Tue, Jun 01, 2004, Jiten wrote:
>
> I am a bit confused is setting the input file for Free energy using
> thermodynamics intergration in sander (amber8). Am I going to run idependent
> MD's with diffferent clamda values for the choice of my n-values. For the MD
> of the next clamda - should start from the restart file of the previous
> clamda value? Or is it possible to combine in one input file? Can anybody
> provide me a sample input file for the same.
>

Below is a perl script that automates the process of running equilibration
and production runs for a variety of lambda values. We do start the "next"
lambda at the end of the "current" one, but that is not a requirement.

Obviously, you would have to modify this script to match your own needs, but
maybe this would give you a start.

...regards...dac

#! /usr/bin/perl -w

# put the values of lambda that you want into the following array:
@clambda=( 0.05, 0.15, 0.25, 0.35, 0.45, 0.55, 0.65, 0.75, 0.85, 0.9, 0.92,
0.94, 0.96, 0.98, 0.99 );

foreach $in ( 0 .. 14 ){

$out = $in + 1;

# equilibration:

open( MDIN, ">mdin");

print MDIN <<EOF;
  diasppear toluene
 &cntrl
   ntr=0,
   nstlim =20000, nscm=2000, ntave=5000,
   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 = 10000, ntwx=0,
   icfe=1, clambda=${clambda[$in]}, klambda=6,
   cut=9.0,
 &end
EOF

close MDIN;

system("mpirun -np 2 /export/wigner/amber8/exe/sander -O -i mdin -p prmtop.vdw -c eq$in.x -o eq$out.oe -r eq$out.xe < /dev/null" );

# production:

open( MDIN, ">mdin");

print MDIN <<EOF;
  diasppear toluene
 &cntrl
   ntr=0,
   nstlim =100000, nscm=2000, ntave=5000,
   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 = 10000, ntwx=0,
   icfe=1, clambda=${clambda[$in]}, klambda=6,
   cut=9.0,
 &end
EOF

close MDIN;

system("mpirun -np 2 /export/wigner/amber8/exe/sander -O -i mdin -p prmtop.vdw -c eq$out.xe -o eq$out.o -r eq$out.x < /dev/null" );

} 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================
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