GROMACS version: 2024.4
GROMACS modification: No
Hi everyone, I was thinking of this past post, which is a bug our group spotted, and that was fixed in the latest gromacs 2024.4 version:
Is gmx bar reading dH/dl contibution from masses?
I wonder what this means for the publications on mutation free energy. As far as I know, these parameters are some needed to properly compute it: couple-intramol = yes , vdw-lambdas , coul-lambdas , bonded-lambdas and, finally mass-lambdas series (the latter 4 set to a series different from merely zeros). The first parameter is necessary to consider the contribution of the internal energy of the amino acids (starting one, and mutated) to the total G value of the protein (WT, and mutant). The bonded and mass ones follow accordingly for analogous reasoning (if I am wrong, I am of course here to learn).
Given that the mass variation due to lambda progression from 0 to 1 was not counted in the DG value until the latest gromacs, the kinetics contribution during the mutation was not there, as we indeed verified when reporting. Am I right? Given that many papers have been published on the topic anyway, I think I must be missing something.
Thank you all for your time, and help.
Bests,
Jacopo