[gmx-users] dimer split
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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