Dear Justin, Where can I find the primary literature for setting up proper parameters in mdp files? I downloaded all literatures in "General Information" section in link below (http://ffamber.cnsm.csulb.edu/ffamber.php), but I did not find anything related to the Cutoffs.
Regards Hassan On Sun, Jun 28, 2015 at 10:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/28/15 3:22 PM, Vidyalakshmi CM wrote: > >> Hi, >> >> You may use the mdp files from the tutorial >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ >> (It has topologies for energy minimzation, nvt and npt simulations and md >> simulations run). >> >> > The tutorial .mdp settings are for OPLS-AA and may not be generally > applicable to any other force field. This is a non-trivial consideration > in running simulations properly. > > "AMBER force field" is a bit generic; different parameter sets use subtly > different parameters. The primary literature for the parameter set of > interest will contain the proper run settings. Use whatever those settings > are. > > -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.
