[moleculetype] UREA 1 looked odd. Why do you only want to exclude singly bonded neighbours from being nonbonded interactions?
Mark On Wed, Feb 5, 2014 at 4:18 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/5/14, 12:11 AM, Gabriele Lanaro wrote: > >> I attached them but I think they didn't pass through. I put the three >> files >> (topol.top, eq.mdp, urea.gro) on this gist: >> >> https://gist.github.com/gabrielelanaro/8817709 >> >> > Nothing glaring sticks out, but here are a coupling things to do: > > 1. With a single molecule in a small box, don't use pressure coupling. > 2. Try a single-point energy calculation to see which of the energy terms > is out of place; it will help you sort out where the issue is. > > http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy > > -Justin > > >> >> On Tue, Feb 4, 2014 at 6:53 PM, Justin Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu>> wrote: >> >> >> >> On 2/4/14, 9:17 PM, Gabriele Lanaro wrote: >> >> Hi! I'm trying to write a custom topology for the urea molecule. >> Taken from >> the following paper http://pubs.acs.org/doi/abs/__ >> 10.1021/jp030534x >> <http://pubs.acs.org/doi/abs/10.1021/jp030534x>. >> >> >> I generated the bonds, angles, torsional dihedrals and improper >> dihedrals. >> The scenario is as follows: >> >> 1) If I leave the bonds section the thing works with or without >> constraints >> 2) If I include the angles and leave constraints off. It works. >> If I put >> constraints on, it gives segfault due to lincs errors. >> 3) If I include the dihedrals it doesn't work, with or without >> LINCS >> >> The simulation consists in a single urea molecule, I used a >> really small >> timestep to figure out what's happening. >> >> I'm having hard time spotting where the problem exactly is and >> how to solve >> it. Any help would be appreciated. >> >> >> You'll need to post the actual topology you have produced in order >> for us to >> comment on it. Perhaps something obvious is wrong, but we won't be >> able to >> tell. >> >> -Justin >> >> -- >> ==============================__==================== >> >> >> Justin A. Lemkul, Ph.D. >> 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 >> >> jalemkul@outerbanks.umaryland.__edu >> <mailto:jalem...@outerbanks.umaryland.edu> | (410) 706-7441 >> http://mackerell.umaryland.__edu/~jalemkul >> <http://mackerell.umaryland.edu/~jalemkul> >> >> ==============================__==================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/__Support/Mailing_Lists/GMX-__Users_List >> <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before >> posting! >> >> * Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists >> >> <http://www.gromacs.org/Support/Mailing_Lists> >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/__mailman/listinfo/gromacs.org__ >> _gmx-users >> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> >> or send >> a mail to gmx-users-requ...@gromacs.org <mailto:gmx-users-request@ >> gromacs.org>. >> >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > 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.