[gmx-users] Wrapping of protein molecules during simulation

Justin Lemkul jalemkul at vt.edu
Wed Aug 28 02:07:28 CEST 2013

On 8/27/13 8:02 PM, Gianluca Interlandi wrote:
> Hi!
> I noticed that gromacs breaks molecules due to PBC during the output of
> trajectories. I understand that this can be fixed with trjconv. Is there any
> option in the parameter file to force gromacs to keep molecules whole? If not is
> it for efficiency purposes?

Doing so serves no functional purpose, so there is no reason mdrun should waste 
time reconstructing molecules during the run (obtaining atomic positions from 
domains, reconstructing from the topology, etc).  Many analysis tools don't even 
require "whole" molecules anyway; it's primarily a visualization convenience.



Justin A. Lemkul, Ph.D.
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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