On 7/11/16 1:30 AM, amitbe...@chemeng.iisc.ernet.in wrote:
Hello,
After a run usually the molecules seems to be broken due to PBC . Do I
need to convert this .gro file into another .gro file with whole molecule(
using trjconv) before the next step. Will there be any difference in
simulation results ?
The final snapshot (e.g. confout.gro) should be intact, but no, it should not
make a difference. The topology always dictates the interactions, and those do
not depend on visualization convenience.
-Justin
--
==
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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