wait, I only changed the cofactor to gromacs charmm27.ff format
On Tue, Jun 10, 2014 at 1:58 PM, Rafael I. Silverman y de la Vega < rsilv...@ucsc.edu> wrote: > I suppose something might be wrong with the simulations. I am using > gromacs 4.6.5, I am simulating a protein with a cofactor, someone else > parametrized it, I changed from charmm to gromacs amber99sb.ff format with > a script on the gromacs website. I did a typical em/nvt/npt equilibration > followed by a 5 ns production run. I picked 250 frames out of the > trajectory, and altered them to the TPIC input format with a script I > wrote, to insert the particle half way between two atoms that I chose. I am > inserting a water molecule. When I run the actual insertion some of the > frames have a reasonable looking mu, and some have -inf mu. I think it may > have to do with cavity size, some frames have too small of a cavity, so the > interaction energy of the inserted water diverges... > > > On Mon, Jun 9, 2014 at 6:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 6/9/14, 6:41 PM, Rafael I. Silverman y de la Vega wrote: >> >>> Hi all, I am having a problem with -inf mu coming out of TPIC >>> calculations. >>> Anyone have some suggestions on how to avoid this? Tabulated potentials? >>> Or >>> can I modify the source code to reject the absurd values that cause >>> this? I >>> read a few old discussions on this, I didnt see much on how to handle >>> this. >>> >>> >> I'd be much more concerned that something is going wrong in the >> simulations. I have no experience with TPIC, but if you post more detailed >> information about what you're doing and which Gromacs version you're using, >> you're more likely to get some suggestions. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 601 >> 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.