[gmx-users] Periodic Boundary removal in Coarse Grains Simulations
jalemkul at vt.edu
Sat Feb 22 18:52:05 CET 2014
On 2/22/14, 12:43 PM, Nikhil Agrawal wrote:
> Hi All,
> I have simulated a membrane proteins system using coarse grain model. after
> simulations when i removed periodic boundary from my simulations box but
> the protein is moving up and down in the box ? I have tried all the
> options nojump ,mol,whole ...etc. no options seems to work.
Without the exact sequence of commands, it's not possible to suggest where you
might have gone wrong. Note that multiple passes to trjconv are typically
> there is something wrong with my trajectory or it is normal with CG ?
Periodicity effects do not depend on the force field. It is certainly possible
that your box is too small for the system being considered, thus the PBC
algorithms in trjconv can't reconcile things (and in that case, your trajectory
would suffer from minimum image violations). What are the dimensions of your
box, and how much space exists between the protein and the box edges?
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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