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?
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 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 Cheers James On Sun, Oct 19, 2014 at 2:05 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/18/14 8:51 AM, James Lord wrote: > >> Hi Justin, >> Thanks for the prompt answer. I selected LJ-(SR) but I am getting a >> positive fluctuating line over the simulation time. Looking at the vmd >> movie I can see that protein (Lysozyme) is coming into contact with >> surface >> afte 10ns and is 5 nm away at the beginning?? my surface is a not charged >> (polyethylene)?? I'd expect zero energy at beginning and upon touching the >> surface negative value??? any comments? Sorry this has nothing to do with >> Gromacs. >> > > A few things: > > 1. Make sure your index groups are correctly constructed. > 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. > 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) > > > -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.