[gmx-users] Custom urea topology

Justin Lemkul jalemkul at vt.edu
Wed Feb 5 03:54:57 CET 2014

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 tell.



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 | (410) 706-7441


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