[gmx-users] pbc problem

Justin Lemkul jalemkul at vt.edu
Sun Feb 2 17:10:46 CET 2014

On 2/2/14, 7:15 AM, Atila Petrosian wrote:
> Dear Justin and Tsjerk
> you said " Some tools handle PBC properly, some don't ".
> I want to know exactly which tools of gromacs handle PBC properly.
> Can I find these tools in manual?

No, because it's not possible to test every single command that the user might 
issue and keep a reliable database of such information.

> I did simulation of a system containing protein and cnt using gromacs 4.5.6.
> When I see trajectory by VMD, in some frames, protein atoms exit one side
> of box
> and enter opposite side of box. I want to do analysis of trajectory. I do
> not know
> exactly this state is pbc problem or not.

Again, that depends entirely upon the command you're using.  Tools like g_rms 
have problems when molecules are split across PBC.  Other tools like g_dist or 
g_msd handle the situation better.  If the protein is the only problematic 
molecule, it should be rather trivial to fix the PBC issues with trjconv 
-center, trjconv -pbc nojump, trjconv -pbc mol -ur compact, or trjconv -fit 
translation, or perhaps some sequence of those.  Please refer to the PBC link I 
have posted several times this week.



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


More information about the gromacs.org_gmx-users mailing list