On 4/20/17 4:37 PM, lan hoa Trinh wrote:
Dear Mark, I equilibrated my system in NVT, and then plot the potential energy. However the potential energy created with the two topology is not match. Thanks in advance,
MD is chaotic, and even identical topologies will yield different results. If you want to test the equivalence of a topology, you should evaluate a single-point energy of an identical configuration of atoms with the two topologies. That's the only meaningful test.
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy -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.
