Tutorial-l Mailing List

From: Courtney Taylor (courtney.b.taylor_at_gmail.com)
Date: Mon Sep 20 2010 - 13:55:06 CDT

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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