[gmx-users] Custom urea topology

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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