Re: SMD-extension

From: Ehsan Ban (ehsan.ban_at_gmail.com)
Date: Fri Aug 26 2011 - 08:36:10 CDT

Hi,

NAMD outputs the center of mass for the restrained atoms in smd:

http://www.ks.uiuc.edu/Research/namd/2.8/ug/node48.html#SECTION000128010000000000000

I would say if the structure is not equilibrated enough before the smd is
performed, then the deformation might be dominated by equilibration itself
and not the smd pulling. What I mean is one possibility is that even in case
that smd was not being performed the atom(s) that are being pulled in the
smd case could have displaced themselves.

Regards
Ehsan

On Fri, Aug 26, 2011 at 9:20 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Fri, Aug 26, 2011 at 6:18 AM, MOhan maruthi sena
> <sena.korukonda_at_gmail.com> 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_.
>
> cheers,
> axel.
>
> >
> >
> > Thank you in advance,
> > -Keerthesh
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>

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