[gmx-users] Fumbling in the dark with dihedral pulling

[Justin Lemkul]

On 4/6/20 10:53 AM, Marko Petrovic wrote:
> Thank you.
>
> I updated the mdp file. (Is the dihedral  defined as a pair of planes rather than a triplet of vectors?)

Perhaps my interpretation of the documentation was incorrect; I thought 
the planes were supposed to be defined, but I suppose it's defined by 
vectors instead.

http://manual.gromacs.org/current/user-guide/mdp-options.html#com-pulling


> Unfortunately I still get the segmentation fault and similar warnings. I will try to compile the differences between the sample mdp and the one I used, then see which differences I can not understand and then just ask about those.

Does your simulation run without pulling options? A sanity check is 
wise. Then test with only one dihedral restrained. It's possible 
something is buggy; I don't know how widely used the dihedral pulling is 
used, and I have not used it personally.

-Justin

> With Regards
> Marko Petrovic
> Educator
> Computational Science and Technology
> School of Electrical Engineering and Computer Science
> KTH Royal Institute of Technology
>
> On 6 Apr 2020, at 14:44, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 4/6/20 2:33 AM, Marko Petrovic wrote:
> I figure it might be helpful to see my other files so I include a link:
> https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin
>
>
> Your dihedral definitions are simply incorrect.
>
> pull_coord1_groups = 1 2 2 3 3 4
> pull_coord2_groups = 2 3 3 4 4 5 should be
> pull_coord1_groups = 1 2 3 2 3 4 pull_coord2_groups = 2 3 4 3 4 5 -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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> jalemkul at vt.edu<mailto:jalemkul at vt.edu> | (540) 231-3129
> http://www.thelemkullab.com
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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