Re: AMBER: new leap with old gibbs

From: David A. Case <>
Date: Tue, 6 Apr 2004 17:13:57 -0700

On Tue, Apr 06, 2004, Carsten Detering wrote:
> meanwhile I found out that it is
> >set default oldparmtopformat (manual page 69)

I'm not sure what "it" is in this context; the format of the prmtop file
is unconnected with how perturbed charges are interpreted.
> 'set default gibbs on' does not work and gives the error messages i
> described in the previous mail.

As I said, I cannot reproduce this here. Are you sure you are running
Amber 8 leap? What do you get if you type "help set" at the LEaP prompt?
(You should see a description of "set default gibbs on" ). [I say this
because the error message you report is what you would get if you were
running Amber 7 LEaP.]

> MAy I ask why gibbs was not incorporated in the new amber release anyway? I
> have tried the new TI feature of sander in amber8 and I have the impression
> it is not as 'sophisticated' as the old gibbs..., but I havent tried it in
> much detail yet.
> will there be a new version of gibbs?

Gibbs was a very powerful program when it was first introduced, but it has not
been updated in many years, and had to be retired. It could not handle
"modern" simulation conditions (with PME, or with polarizable potentials, or
with "extra points"). None of the developers was willing to put in the effort
to bring it up do date.

Further (at least in my view) the features that were not carried over from
gibbs into sander are not enormous losses: thermodynamic integration is
generally more efficient that free energy perturbation theory; the complex
schemes used in gibbs when atoms "disappear" can mostly be replaced by a much
simpler approach involving non-linear lambda sampling; niceties like "bond PMF
corrections" are mostly unnecessary with sander; and ordinary PMF calculations
can be carried out more straightforwardly using WHAM than with the original
gibbs approach.

So, there will not be a "new version of gibbs", although some particular
features in it may continue to be introduced into sander as the code


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            |
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Received on Wed Apr 07 2004 - 01:53:00 PDT
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