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

[Justin A. Lemkul]

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
> 
> 

-- 
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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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