You are right it is the name of molecule type in .top, and thus no error upon executing grompp, so index group is constructed correctly right??? rvdw=1 nm so should be fine. and for the last part I agree. Cheers James
On Sun, Oct 19, 2014 at 2:34 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/18/14 9:30 AM, James Lord wrote: > >> Hi Justin, >> >> 1. Make sure your index groups are correctly constructed. >> Do I need to use make ndx? I thought just adding energygrps=protein >> surface >> at the end of .mdp is enough? >> >> > "Surface" isn't likely a default group (unless that's the name of the > [moleculetype]) and grompp should have raised a fatal error if the group > wasn't defined. > > 2. What does 5 nm correspond to? A COM distance? A minimum distance? If >> the latter, then the LJ-SR energy should likely be zero, but if it's a COM >> distance, that's not necessarily the case. >> 5 nm is minimum distance >> >> > OK, in this case, the initial LJ-SR should be zero, provided that rvdw < 5. > > 3. Is your PE model united-atom or all-atom? If the latter, you still >> have >> partial charges that will contribute to a negative Coul-SR (of course, >> this >> is something you can check very simply >> It is all atom >> > > Then you must have partial charges on the individual atoms and therefore > Coul-SR will be non-zero. > > > -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.