[gmx-users] Custom urea topology

[Gabriele Lanaro]

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



On Tue, Feb 4, 2014 at 6:53 PM, Justin Lemkul <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 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 at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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