BAR calculation

User discussions
1

GROMACS version: module load gromacs/2020.2-cpu
GROMACS modification: Yes/No
Here post your question

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

2

Looking at videos will not tell you much.

Depending on the size of the part you are transforming, you might need much longer simulations and you need to have suitable free-energy parameters and spacing of the lambda points.

3

Thank you very much for your help.
I will perform longer simulations and check the parameters and spacing of the lambda points.

Best regards,
Asaf