[gmx-users] Regarding periodic boundary condition

[Justin Lemkul]

On 7/11/16 1:30 AM, amitbehra at 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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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