Thank you Dr. Lemkul, I am trying to run grompp with the md integrator, but I am getting this error: "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used"
Should I ignore this warning with the -maxwarn option and try running it? I will see if I obtain comparable values for ethanol. Best Regards, Dan On Mon, Mar 27, 2017 at 12:51 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/26/17 9:40 PM, Dan Gil wrote: > >> Hi, >> >> I am following Dr. Sander Pronk's and Dr. Justin Lemkul's tutorial on >> calculating free energy of solvation. Is it possible and theoretically >> sound to use the md integrator instead of the sd integrator for these >> calculations? >> >> > Langevin dynamics gives better sampling so it is frequently used for free > energy calculations. You may get comparable results with the leap-frog > integrator, but I haven never done a side-by-side comparison. > > -Justin > > I have already done a considerable amount of work using md integration, and >> I want to make sure that the free energy values I calculate are consistent >> with my previous work. >> >> If using the md integrator is not sound, is there an alternative way of >> calculating solvation energy that will be consistent? >> >> Best Regards, >> >> Dan >> >> > -- > ================================================== > > 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.