On 6/22/17 8:56 AM, Sergio Manzetti wrote:
HI, I use mdp for simulating with a 2fs time step, nstlist 10, rlist 1.2, rcoulomb 1.2, rvdw 1.2, V-rescale, no P-coupling. Lincs on all bonds, still the DNA system won't minimize . What is your experience with DNA simulations and these settings? Do you have an mdp file that may be generally good for DNA sims?
Settings depend on the force field, not the molecules in the system. If you want commentary, please provide a full .mdp file, not just select settings.
-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.
