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.
-Justin
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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
