Mark, we just figured it out, thanks. :) And yes, you are definitely onto something: two identical dihedrals pulling in opposite directions. This is what happens when people from solid state show up to use GMX. :)
Alex On Tue, Apr 14, 2015 at 5:20 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Can you shift it to 40 degrees? > > Mark > > On Tue, Apr 14, 2015 at 11:26 PM, Alex <nedoma...@gmail.com> wrote: > > > Absolutely nothing in between, this is (cos(45)-cos(phi))^2, two minima > at > > 45 and 315 and a peak around 180. Checked if I converted to R-B > > coefficients correctly -- same thing. At 90/270 clean decrease to 45/315. > > > > Alex > > > > > > On Tue, Apr 14, 2015 at 3:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 4/14/15 5:12 PM, Alex wrote: > > > > > >> Tried both, the (now enormous) parameters are read in correctly, > nothing > > >> in > > >> output mdp that catches my eye. No constraints used in the system, > > >> explicitly set in mdp. Plotted the potential at 45/315 deg minimum -- > > >> definitely nonzero at 90 degrees (starting config). This has got to be > > the > > >> strangest GMX issue i've ever had. > > >> > > >> > > > What does a 1-D energy surface look like for that dihedral? You've > got a > > > dihedral at 90 in the coordinates and you're trying to shift it to 45? > > If > > > there's a massive barrier in between, EM won't necessarily do that for > > you. > > > > > > -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. > > > -- > 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.