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Bug #2609

Evaluating PMF for angle rotations using gmx WHAM

Added by Jonathan Sheavly over 1 year ago. Updated 5 months ago.

Status:
Closed
Priority:
Low
Assignee:
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
simple
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Description

I had been trying to evaluate a PMF using umbrella sampling (GROMACS 2016) for rotating an object. The mdp option I used was:
pull_coord1_geometry = angle-axis

The .mdp options page says the input units are in degrees, and the simulation runs fine with this. However, when evaluating the PMF using gmx WHAM, the histograms seemed to overlap in x space, but not in force space which yields "nan" PMF results.

After troubleshooting, I found that the tpr file input for WHAM is required to be in radians (but is read in degrees within GROMACS simulations) and the pull-f files then can be used to get reasonable PMFs. Right now my workflow is fully functional, but I thought other would like to know how to fix this.

The only fix would be some conversion within WHAM from degrees to radians when reading the tpr files. I hope this helps to continue to improve GROMACS analysis tools


Related issues

Has duplicate GROMACS - Bug #2903: gmx wham doesn't compute profile with pull=angle-axisClosed

Associated revisions

Revision 7e3521c2 (diff)
Added by Berk Hess 5 months ago

Fix gmx wham with angle geometries

Fixes #2609

Change-Id: I36156e1d8bb98499e4357eadc4ca56384da433a5

Revision 592be1a9 (diff)
Added by Berk Hess about 2 months ago

Actually fix gmx wham with angle geometries

A previous fix for converting the force constant in gmx wham
for angle and dihedral geometry applied an incorrect conversion
factor.

Fixes #2609 and #3094

Change-Id: I0aa9b848c7fa62306ccf15b327a650b1ad88e03f

History

#1 Updated by Berk Hess 5 months ago

  • Has duplicate Bug #2903: gmx wham doesn't compute profile with pull=angle-axis added

#2 Updated by Berk Hess 5 months ago

  • Status changed from New to Fix uploaded
  • Assignee set to Berk Hess
  • Target version changed from future to 2019.3

I uploaded a fix, please check:
https://gerrit.gromacs.org/c/gromacs/+/11458

#3 Updated by Berk Hess 5 months ago

  • Status changed from Fix uploaded to Resolved

#4 Updated by Paul Bauer 5 months ago

  • Status changed from Resolved to Closed

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