[gmx-users] pbc

[Justin Lemkul]

On 1/31/14, 7:09 AM, kannan wrote:
> Thank you for your reply Tsjerk..
> I do many Trjconv -pbc mol -ur compact -center. but it doesn't help..
>
> this is PBC. if i center protein the ligand goes other side at end of
> simulation. if i center ligand, then protein goes... if i center both, its
> trajectory is same as old one.
>
> How to overcome this problem? Please give some suggestion.
>
> or shall i analyse without trjconv -pbc with raw trajector?
>

As Tsjerk said, some tools handle PBC well, some don't.  If you're having a 
specific issue with a specific tool, then you will need to account for 
periodicity effects.  If not, then there is no need to worry.  With 
protein-ligand systems and other complexes, -pbc nojump is usually the best 
first step.  See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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