[gmx-users] Custom urea topology
jalemkul at vt.edu
Wed Feb 5 16:20:34 CET 2014
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:
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.
> On Tue, Feb 4, 2014 at 6:53 PM, Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at 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
> 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
> 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 at outerbanks.umaryland.__edu
> <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
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Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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