Suggested steps for calculating entropy in solution and binding
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 2 years 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?