[gmx-users] Pull simulation odditites when viewed in VMD

[Natalie Stephenson]

Thanks loads for that!! I hadn't realised it was that simple!
Natalie
xxx

________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 09 December 2010 12:05
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Pull simulation odditites when viewed in VMD

Natalie Stephenson wrote:
> Hey,
>
> I've been performing a pull simulation of a protein, all seems to work
> fine however after I convert the .xtc file into seperate .gro files and
> load those into VMD to visualise the simulation something weird
> happens.  Every 50 frames or so a random bond within the backbone of the
> protein (not necessarily near the point of pulling or unfolding) seems
> to extend and spike out massively from the structure - does anyone know
> why that would be happening?
>

Please see FAQ #9:

http://www.gromacs.org/Documentation/FAQs

-Justin

> Thanks for your help
> Natalie
>
>

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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