Dear Justin, How could I change the cut-offs to make the MD more faster in my case?
/Urszula > > > On 6/3/14, 4:15 AM, Urszula Uciechowska wrote: >> Dear Gromacs users, >> >> I would like to run simulations with implicit water. My protein system >> is >> quite big it contains 784AA. I prepared eM.mdp file (see below) however >> I >> am not sure if its ok especially the rlist what should I use there in >> case >> of such big system. >> >> define = -DFLEXIBLE >> constraints = none >> integrator = steep ; steepest descents energy >> minimization >> dt = 0.001 ; ps >> nsteps = 3000 ; maximum number of steps to >> integrate >> implicit_solvent = GBSA >> gb_algorithm = Still >> nstgbradii = 1 >> gb_epsilon_solvent = 80 >> gb_saltconc = 0 >> sa_algorithm = Ace-approximation >> sa_surface_tension = -1 >> pbc = no >> rgbradii = 0 >> ns_type = simple ; method of updating neighbor >> list >> nstlist = 0 >> rlist = 0 ; this means all-vs-all (no >> cut-off) >> coulombtype = cut-off >> rcoulomb = 0 ; [nm] distance for Coulomb >> cut-off >> vdwtype = cut-off ; twin-range cut-off with rlist >> where rvdw >= rlist >> rvdw = 0 ; [nm] distance for LJ cut-off >> nstenergy = 100 >> emtol = 5.0 >> emstep = 0.01 >> comm-grps = Protein >> optimize_fft = yes >> >> Thank you in advance for any comments and suggestions. >> > > If you're using infinite cutoffs, the only acceptable value for rlist is > 0. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > 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. > > ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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.