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.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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Received on Tue Jun 01 2004 - 20:53:00 PDT
