I use the AMBER99SB-ILDN ff for a piece of DNA taken from the RCSB database. Removed all waters and non-nucleic acid molecules, and everything seems fine.
The mdp settings are: title = DNA in water stabilization cpp = /lib/cpp include = -I../top define = integrator = md dt = 0.002 nsteps = 5000000 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 300 nstxout-compressed = 300 compressed-x-grps = DNA SOL NA CL energygrps = DNA SOL NA CL nstlist = 10 ns-type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 tcoupl = V-Rescale tc-grps = DNA SOL NA CL tau-t = 0.1 0.1 0.1 0.1 ref-t = 310 310 310 310 Pcoupl = No tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 gen-vel = yes gen-temp = 310 gen-seed = 173529 constraints = all-bonds Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, June 22, 2017 3:07:03 PM Subject: Re: [gmx-users] MDP for DNA with ions 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. -- 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.