AMBER Archive (2004)

Subject: Re: AMBER: Free energy in Amber8

From: Jiten (jiten_at_postech.ac.kr)
Date: Tue Jun 01 2004 - 20:02:40 CDT

Dear Professor David,

I quite do not understand the meaning of production run for the free energy
MD. Is it has the same meaning as in Sander MD prior to the equlibration. My
starting coordinate file is from the previously performed 1ns equlibration.
For such case do I need to run the production for each step of the lamda
value or just at the beginning of the peturbation when lamda=0

Thanking you,

Sincerely,

JIten
----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Wednesday, June 02, 2004 4:17 AM
Subject: Re: AMBER: Free energy in Amber8

> 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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