[gmx-users] PBC

Justin Lemkul jalemkul at vt.edu
Sat May 6 00:52:57 CEST 2017

On 5/5/17 1:37 PM, Alex wrote:
> Dear Gromacs user,
> I want to study the interaction between a nanoparticle(5 nm diameter) and
> some heptapeptide around the nanoparticle in aqueous solution. I put
> the nanoparticle
> in the center of a box and the rest are around it.
> I was wondering if I should use PBC (periodic boundary condition) in such a
> system? What is the advantage of the using PBC here?

The same as any system - you don't have boundary effects and your system won't 
turn into a quickly evaporating droplet.


> The disadvantage of using PBC here is that a very big box should be used to
> avoid interaction between a peptide and another peptide in the adjacent
> cell.
> Regards,
> Alex


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


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