[gmx-users] Custom urea topology

[Mark Abraham]

[moleculetype]
UREA 1

looked odd. Why do you only want to exclude singly bonded neighbours from
being nonbonded interactions?

Mark


On Wed, Feb 5, 2014 at 4:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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>
>>
>>     ==============================__====================
>>
>>     --
>>     Gromacs Users mailing list
>>
>>     * Please search the archive at
>>     http://www.gromacs.org/__Support/Mailing_Lists/GMX-__Users_List
>>     <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before
>> posting!
>>
>>     * Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>>
>>     <http://www.gromacs.org/Support/Mailing_Lists>
>>
>>     * For (un)subscribe requests visit
>>     https://maillist.sys.kth.se/__mailman/listinfo/gromacs.org__
>> _gmx-users
>>     <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
>> or send
>>     a mail to gmx-users-request at gromacs.org <mailto:gmx-users-request@
>> gromacs.org>.
>>
>>
>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>