[gmx-users] PBC problems??

Justin Lemkul jalemkul at vt.edu
Fri May 23 22:44:21 CEST 2014

On 5/23/14, 2:51 PM, Steve Seibold wrote:
> My protein breaks according to viewing the traj in VMD and graphing the RMSD of the protein C-terminus
> I have tried all combinations of "trjconv -pbc -center
> -box center" and nothing works..I was able to get online and find a
> tutorial that says trjconv -pbc mol, should stop the problem, but this
> failed....Isn't there a way for the protein and water to be wrapped or COM
> calculations done DURING MD to remove translation, rotation so that post-MD
> modification of trajectories is unnecessary??...If I make an index group of the

The integration doesn't need to follow our visualization convenience, so there's 
no reason to sacrifice performance to re-wrap coordinates on the fly.

> N-terminus of the protein this problems goes away or if I use the whole
> protein...It is only when I attempt to get the rms of the C-terminus region
> that I get this graphing problem (traj plots look like Histograms)....Not sure what this means since if I observe
> the trajectories in VMD the whole protein breaks up....

Centering a single protein within a box should be very easy using any of the 
options you have posted.  trjconv -pbc mol -ur compact -center should be all 
that's necessary for a simple system like this.  Are you sure the box is large 
enough to accommodate the protein?  If it keeps "breaking" in spite of trjconv, 
that might suggest your box is not suitable, such that re-imaging can't fix things.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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