Re: SMD-extension

From: Axel Kohlmeyer (
Date: Fri Aug 26 2011 - 08:20:28 CDT

On Fri, Aug 26, 2011 at 6:18 AM, MOhan maruthi sena
<> wrote:
> Hello everyone,
>                         I am using smd to pull a peptide  surrounded by a
> protein.When i see the output file instead of extension , it is getting
> contracted.Can you please explain me why is it so?

isn't it obvious that you are likely using the wrong sign somewhere,
e.g. when specifying the pulling direction vector? ;)

MD (and that includes SMD) strictly adheres to the
"garbage-in-garbage-out" principle. particularly when
using a code that has been used successfully a _lot_.


> Thank you in advance,
>  -Keerthesh

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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