[gmx-users] RE:Stopping protein jumping inside box?

[Justin Lemkul]

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On 2/14/13 11:54 AM, 라지브간디 wrote:
>
> I have tried -pbc nojump, and other options given in that link but still my protein gets jumped! Plz guide me, how to stop this ?

The suggested trjconv workflow is here:

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

If you want specific help, you're going to have to provide exactly the sequence 
of commands you are issuing and a description (or better, link an image) of 
what's going on and why it's not satisfactory.  Otherwise, there is nothing 
anyone can say except that you're not doing something right.  Nearly every 
protein-in-water system (ligand or not) can be re-imaged suitably with:

1. trjconv -pbc nojump
2. trjconv -pbc mol -ur compact -center

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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