[gmx-users] Fixing periodicity effects on trajectory file

Justin Lemkul jalemkul at vt.edu
Tue Sep 15 13:42:50 CEST 2015

On 9/15/15 7:39 AM, Homa rooz wrote:
> Hi there
> I'm working with gromacs for ligand-protein interaction simulation. I have
> run MD for docked complex and now there is a problem with trajectory
> visualization by VMD. The ligand has left binding site circulating around
> the protein.
> I tried to fix the problem by making index and extract the first frame from
> the trajectory to use as  reference and also running "-center", "no jump",
> "no pbc", "-fit rot" but the problem still exists. I'm quite confused.
> Should I execute fixing command in the special order?
> Which group is more preferred to be located at the center,Protein or
> system(non-solvent)?

If the system is a simple binary protein:ligand complex in water, trjconv 
-center -pbc mol should do it.  Center on the protein, output whatever is 
meaningful to you.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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