From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Sep 20 2010 - 15:07:28 CDT

Can you send me a tar/zip of all your files (off-list) so I can take a look? I guess it's pretty small.

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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