OK, thanks for this!
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 3:17:02 PM Subject: Re: [gmx-users] MDP for DNA with ions On 6/22/17 9:09 AM, Sergio Manzetti wrote: > 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 AMBER uses shorter cutoffs. Refer to their papers for what is correct. > 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 Don't do this. http://www.gromacs.org/Documentation/Terminology/Thermostats#What_No_To_Do > 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 IIRC AMBER only constrains bonds to H, so again check the literature. None of these points is likely fatal (maybe the thermostat) but you should use correct settings. If your system is crashing with this .mdp file or the corrected one, it's because you haven't adequately minimized and equilibrated. -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.
