Re: Problem with running FEP calculations

From: chipot (
Date: Mon Apr 15 2013 - 00:03:24 CDT


did you "alchemify" explicitly your PSF, or do you let NAMD clean up the
file? In the latter case, I suggest you run "alchemify" separately, as the
symptom you describe looks like the two topologies are "talking" to each
other. Cheers,

Chris Chipot

Chris Chipot, Ph.D.
Beckman Institute. University of Illinois at Urbana-Champaign

sent from my iPad

On Apr 15, 2013, at 1:51 AM, Eric Lang <> wrote:

> Hello,
> I would like to run some alchemical Free Energy Perturbation calculations on a Blue Gene P system. Although my calculations work well on my PC and on a Power 7 cluster they do not work on the Blue Gene system. (NAMD 2.9 used on all platforms)
> I tried different simulations, including the crown ether example from the FEP tutorial, and I always have the same kind of errors with the Blue Gene P:
> I got messages like "Constraint failure in RATTLE algorithm for atom ... simulation has become unstable" at the very beginning of the simulation. If I deactivate the RATTLE algorithm, it works for the first window, but at the beginning of the second window I got the messages “Atoms moving too fast”. (please note that all the simulated systems are well equilibrated)
> I therefore strongly suspect the build of NAMD on the Blue Gene system I am using, but I do no know what can be wrong (classical simulations work well). Does anyone have an idea of what could be the problem? Are there any important thing related to FEP to take care of when building NAMD form source?
> Many thanks in advance for your help,
> Eric
> Eric Lang
> Department of Chemistry
> University of Canterbury
> Christchurch – New Zealand

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