On 11/17/16 10:13 AM, Apramita Chand wrote:
Dear All, Thanks for your explanation, Erik. I just want to know whether applying trjconv will affect my calculations of other values like radial distribution functions ,hydrogen bond properties. Before applying trjconv,my protein molecule appears to be shifted partly out of the box . Should I be applying trjconv in this situation before calculation of properties? Is it necessary at all?
Nearly all GROMACS tools handle PBC automatically. Only position-dependent properties like RMSD, RMSF, covariance, etc. are impacted by not accounting for PBC. Anything related to distances like RDF, H-bonds, etc. requires no correction, but even if you do use trjconv, the results should come out the same.
-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 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.
