Thanks for your quick reply. Up till now all the simulations I have performed are with the OPLS force field, because the software I used in the past supported only that in the academic version. Anyway, to sum it up for non bonded from the literature about a particular force field and try some tutorials. Got it. Thank you so much
________________________________________ From: [email protected] <[email protected]> on behalf of Justin Lemkul <[email protected]> Sent: Wednesday, September 2, 2015 12:26 AM To: [email protected] Subject: Re: [gmx-users] mdp file On 9/1/15 12:50 PM, Sotirios Dionysios I. Papadatos wrote: > Hi, > > I am having some trouble defining a proper mdp file for minimization and > production runs. I am aware of the manual's - site's reference to this > matter, it is pretty thourough. > > My question is: How do I know which parameters to use for each simulation? Is > there a publication, book etc to guide the user through this? I mean for > example if I want to simulate a protein, which parameters do I have to use?? > Try some tutorials. http://www.gromacs.org/Documentation/Tutorials Most settings (output, thermostats, etc) are pretty boilerplate. The nonbonded setup (cutoffs) depend on the force field, which you will learn about by reading the primary literature for the force field you've chosen for your work. Because you've scrutinized the literature and know about why you've chosen that particular force field, right? -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 [email protected] | (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 [email protected]. -- 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 [email protected].
