[gmx-users] pbc

[Justin Lemkul]

On 1/5/16 11:58 AM, Parvez Mh wrote:
> Dear all:
>
> I am using pbc in all directions, it is expected that,  i will observe
> broken molecules in central box. But i am wondering, some molecules are out
> of box when i visualize with vmd. What would the right explanation of this?
>

PBC is the explanation.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================