[gmx-users] dimer split

Justin Lemkul jalemkul at vt.edu
Thu Nov 5 17:14:51 CET 2015

On 11/5/15 10:56 AM, xy21hb wrote:
> Dear all,
> I have a two-identical dimer protein, and I am interested in the chain-chain interaction.
> However, after long MD, the two chains are separated far from each other though I used PBC.
> In fact, the chains should be quite close.

You should spend a bit of time reading about what "using PBC" means; your dimer 
isn't actually split.

> I guess GROMACS treats the chains as A and B, and restrain each individually.

You should not restrain chains to fit some preconceived visualization convenience.

> I wonder if there is any way GROMACS  can consider it as a whole, or maybe other solutions.

This is what trjconv is for.  Re-image the trajectory, centering on one of the 
chains or some interfacial residues in one monomer.



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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