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

[Marko Petrovic]

Thank you.

I updated the mdp file. (Is the dihedral  defined as a pair of planes rather than a triplet of vectors?) 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.

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.
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