[gmx-developers] issue on benchmarking FEP calculations in Gromacs and NAMD

[Wang, Yuhang]

Dear Gromacs developers,

I have benchmarked the desolvation free energy calculation of Na+ ion using Gromacs and NAMD (for comparison). There is a large difference in the electrostatic desolvation free energy (see below and the attached figure):

Gromacs: 82.10(raw)+11.65(Ewald correction) = 93.75 kcal/mol
NAMD:     93.62(raw)+11.23(Ewald correction) = 104.85 kcal/mol

Both of them are FEP calculations with perturbation of electrostatic interactions and used the same Lennard-Jones parameters:
sigma=0.243 nm, epsilon=0.196 kJ/mol (0.0469 kca/mol)

Ewald correction was calculated by: 0.5*(2.837297/L)*331 (unit: kcal/mol), "L" is the cubic box length.

Question: how can I explain the difference? Does Gromacs have a different PME implementation than NAMD?

P.S. my input scripts are in the attachments.


Steven W.
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