On 5/24/16 6:35 AM, Antara mazumdar wrote:
Dear gromacs users, I am trying to calculate domain decomposition of a mixed lipid vesicle system OF SIZE 268675 Atoms and box size is 32 X 32 X 32 nm to be able to run in parallel. I want to calculate the number of PME nodes per total number of nodes. However, i am not clear on how to calculate the value of nPME here. I would also mention that number of nodes that can be used need to be multiple of 16 and the value of minimum cell size is 1.8 nm. Can someone guide me in this regard?
Is there something wrong with the number of PME nodes that mdrun sets up by default? -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.