[gmx-users] pbc

Justin Lemkul jalemkul at vt.edu
Fri Jan 31 13:56:14 CET 2014

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 



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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