Re: Gibbs: DynamicWin and NSTMEQ?

From: David A. Case <>
Date: Fri 7 Feb 2003 16:12:07 -0800

On Thu, Feb 06, 2003, Paula Petrone wrote:
> Following the Methane Tutorial I am "disappearing" Water into TIP3P water
> solvent. As I change the NSTMEQ and NSTMUL parameters, the Free energy
> varies completely (from the value in Literature -6 kcal) but still, the
> difference between the "forward" and "backward" results are very close.
> Increasing NSTMEQ and NSTMUL is affecting the convergence value!
> How can I get a "reliable" result?

First, I should say that I hardly ever use Gibbs (and I think that is true
of most other current Amber developers), so that it is difficult for us
to give detailed help.

But in general, you would need pretty large values of NSTMEQ and NSTMUL to
get converged results (I'd think in the 10000 - 50000 range). Also, using
a CUT value of 6.0 is way too short...there are many important interactions
that are longer than this...something in the 12-14 Ang. range is probably

If you haven't used gibbs a lot, try reproducing some literature calculations,
for example:

%A D.A. Pearlman
%T A comparison of alternative approaches to free energy calculations
%J J. Phys. Chem.
%V 98
%P 1487-1493
%D 1994

%A Y. Sun
%A D. Spellmeyer
%A D.A. Pearlman
%A P. Kollman
%T Simulation of the solvation free energies for methane, ethane, and
propane and corresponding amino acid dipeptides: A critical tes of the
"bond-PMF" correction, a new set of hydrocarbon parameters, and the gas
phase-water hydrophobicity scale
%J J. Am. Chem. Soc.
%V 114
%P 6798-6801
%D 1992

Remember that getting absolute solvation free energies (by "disappearing"
something to nothing) is one of the most difficult of free energy tasks.
I'd also suggest (but perhaps I am biassed) that you consider sander rather
than gibbs for a task like getting the absolute solvation of water in water.
See the Users' Manual, section 5.6.18.

.hope this helps...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            |
Received on Fri Feb 07 2003 - 16:12:07 PST
Custom Search