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Feature #2667

Suggested steps for calculating entropy in solution and binding

Added by Magnus Lundborg 10 months ago. Updated 9 months ago.

Status:
New
Priority:
Normal
Category:
documentation
Target version:
Difficulty:
simple
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Description

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.

History

#1 Updated by David van der Spoel 10 months 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 10 months 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 9 months ago

Seems too late for 2019 now?

#4 Updated by Magnus Lundborg 9 months ago

  • Target version changed from 2019 to 2020

#5 Updated by David van der Spoel 9 months ago

The code has been restored in https://gerrit.gromacs.org/#/c/8482/
A description how to do it is in https://pubs.acs.org/doi/abs/10.1021/ct400404q
I could still try to add it to the manual.

#6 Updated by Magnus Lundborg 9 months 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.

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