Tutorial-l Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Sep 20 2010 - 16:24:38 CDT

Okay, now I remember this part. The forward/backward configuration files include a minimization step, accomplished by using the command "runFEPmin". A separate minimization step isn't necessary, although if you wanted to run it anyway, you'd have to add the relevant FEP lines to the configuration file (with your starting and ending lambda values both being 0 or 1).

JC

On Sep 20, 2010, at 1:55 PM, Courtney Taylor wrote:

> I looked through the archives, but it seems no one else had an issue with this yet.
>
> I am running namd 2.7b2 and trying to reproduce the Tyr to Ala mutation portion of the tutorial. When I try to minimize the vacuum system, the simulation crashes on the following:
> LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
> LINE MINIMIZER BRACKET: DX 0 0 DU nan nan DUDX nan nan nan
>
> From the namd mailing list, I see that this is sometimes caused when atoms overlap, which is somewhat automatic in the current situation with hybrid atoms/dual topology. I'm using all the files provided online for comparison, so I'm not sure why it is not working. Is there a step I am missing?
>
> The solvated system minimization and runs work great.
>
> Thanks,
>
> Courtney Taylor
> PhD Candidate
> Department of Chemical and Biomolecular Engineering
> Vanderbilt University
>

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