Feature #2667

Suggested steps for calculating entropy in solution and binding

Added by Magnus Lundborg over 1 year ago. Updated 4 months ago.

Target version:


I think it would be good to include in the manual (or in the gmx anaeig/covar tools) a brief guide to how to calculate the entropy of a molecule/ligand in solution and while binding to e.g. a protein. Previously it was suggested to do a gmx trjconv -pbc nojump -ur compact. Is that still needed now that gmx covar can apply corrections for pbc? When running gmx covar what groups make sense to fit - should any groups be avoided?

There seems to be a fair amount of interest in calculating entropy, and some questions are asked how to do it or why the results seem wrong, but there is often no conclusion reached. It would be good to list best-practice.


#1 Updated by David van der Spoel over 1 year ago

I would say there is little physics behind it and therefore this must be discouraged. The best way is to a potential of mean force or otherwise free energy calculation at multiple temperatures.
I can propose some text for the latex manual, or where should it go?

#2 Updated by Magnus Lundborg over 1 year ago

If it should be discouraged that would indeed be good to note. I think giving a brief list how to do it best in the LaTeX manual would be appreciated by many.

#3 Updated by Mark Abraham over 1 year ago

Seems too late for 2019 now?

#4 Updated by Magnus Lundborg over 1 year ago

  • Target version changed from 2019 to 2020

#5 Updated by David van der Spoel over 1 year ago

The code has been restored in
A description how to do it is in
I could still try to add it to the manual.

#6 Updated by Magnus Lundborg over 1 year ago

This feature request is not about the restored code (that was a separate issue). At least a reference to that publication would be good, but a brief instruction in the manual would be helpful.

#7 Updated by Paul Bauer 6 months ago

  • Target version changed from 2020 to 2020.1

documentation targeted on first 2020 patch release

#8 Updated by Paul Bauer 4 months ago

  • Target version changed from 2020.1 to 2020.2

bump, Magnus is this planned for 2020 patches or in master?

#9 Updated by Magnus Lundborg 4 months ago

I don't know. I just requested this feature since I don't know the proper process and people wonder on different mailing lists.

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