Re: AMBER: zero free energy change for nonbond leg of electrst. decoupling

From: David A. Case <>
Date: Tue, 5 Aug 2003 12:39:22 -0700

On Tue, Aug 05, 2003, Alfonso Garcia Sosa wrote:
> I have been running some free energy perturbations
> (thermodynamic integration, dynamically modified windows) with
> electrostatic decoupling in gibbs (that came with amber7) and
> had no problems during the first leg, ielper = 1, that is,
> change in electrostatics and nothing else. For the second leg
> (change in vdW and other non-electrostatics, fixed electrostatics),
> I set ielper = -1, and started a new run. The problem I have is that
> the values for energy changes are all zero for the whole length of
> the new run and also after completion.

> Quantities used in integration:
> <dV/d_lam> = 0.38978385E-15 <V(lam-dep.)> = 165.62357

Is it possible that your unperturbed and perturbed systems differ only
in their charges? This would explain getting zeroes for <dV/d_lam> and
for the total change.

This is just a wild speculation...otherwise, I don't see what is going on.
If this isn't the problem, try just regular TI (without the dynamically
modified windows), e.g. idifrg=1, isande=1, just asking for a single
window. You'll need just a few integration steps to see if you are still
getting all zeroes...

...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            |
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Received on Tue Aug 05 2003 - 20:53:01 PDT
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