AMBER Archive (2004)

Subject: Re: AMBER: About the free energy difference in vacuum with GIBBS.

From: David A. Case (
Date: Wed Jul 14 2004 - 15:51:38 CDT

On Mon, Jul 12, 2004, Chunhu Tan wrote:
> I want to calculate the free energy difference between H3C-SH and H3C-OH in
> vacuum. With xleap, I built two sets of .pert_top and .inpcrd files: H3C-SH
> -> H3C-OH and reverse, and then minimized and equilibrated them with the
> same input files. After that, I GIBBS them with also the same input
> file.(All input files as shown below). As I thought, the results of this
> two simulations will be almost the same except the sign, but my results were
> entirely different.

I don't see any obvious problem. You will need to look carefully at the
outputs. In particular, check the two directions for lambda=1/2, which should
be using the same potential function: see if you can isolate any differences
between the forward and reverse directions. You should be able to start
simulations from identical conditions with the two different prmtop files,
and see equivalent dynamics (I think!).

Since you are running TI calculations, you could cross-check the gibbs results
by running sander as well.

...good luck...dac


================================================================== David A. Case | e-mail: 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to