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.
