[gmx-users] carbon nanotube - ifnite in length ?

Justin Lemkul jalemkul at vt.edu
Thu Sep 26 22:28:12 CEST 2013

On 9/26/13 10:19 AM, Dr. Vitaly Chaban wrote:
> I am just curious why the system would explode without
> "periodic_molecules = yes". If the PBC procedure is applied before
> harmonic bond potential is calculated, than the opposite nanotube
> atoms should be (already) seen as neighboring. This looks the same as
> the solvent molecule, one atom of which crossed the box boundary.
> No?

Without setting the periodic_molecules keyword, mdrun tries to assemble all the 
bonds within the unit cell.  Given that a bond between atoms at either end of 
the box would be very unfavorable, it would distort the system considerably, or 
fail altogether if using constraints.  Bonds only span PBC when instructed with 



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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