BAR calculation – User discussions

GROMACS version: module load gromacs/2020.2-cpu
GROMACS modification: Yes/No
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Dear Gromacs Users,

I hope that all is well.

I have performed free energy transformations and in two cases I got in the Bennet Acceptance Ratio (BAR) calculation:

“WARNING: Some of these results violate the Second Law of Thermodynamics:
This is can be the result of severe undersampling, or (more likely)
there is something wrong with the simulations.”

I have checked the simulation videos and they look ok and in other transformations it worked well.
I was told that it might require normalizing the energies by kT.

I would appreciate your help.

Thank you,
Best regards,
Asaf

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