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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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