[gmx-users] Custom urea topology

[Justin Lemkul]

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 <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
>         <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
>     <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
>     http://mackerell.umaryland.__edu/~jalemkul
>     <http://mackerell.umaryland.edu/~jalemkul>
>
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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
20 Penn St.
Baltimore, MD 21201

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

==================================================