you think it was the cofactor model?
On Tue, Jun 10, 2014 at 2:23 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/10/14, 5:01 PM, Rafael I. Silverman y de la Vega wrote: > >> wait, I only changed the cofactor to gromacs charmm27.ff format >> >> > Pretty amazing that the simulation even ran with that mash-up of > parameters :) > > I'd say that's the most likely cause of your problems; nonsensical > physical model leads to nonsensical output. > > -Justin > > > >> 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. >>>> >>>> >>> >>> > -- > ================================================== > > 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.