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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear Gromacs developers,<br>
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<br>
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):<br>
<br>
Gromacs: 82.10(raw)+11.65(Ewald correction) = 93.75 kcal/mol<br>
NAMD: 93.62(raw)+11.23(Ewald correction) = 104.85 kcal/mol<br>
<br>
Both of them are FEP calculations with perturbation of electrostatic interactions and used the same Lennard-Jones parameters:<br>
sigma=0.243 nm, epsilon=0.196 kJ/mol (0.0469 kca/mol)<br>
<br>
Ewald correction was calculated by: 0.5*(2.837297/L)*331 (unit: kcal/mol), "L" is the cubic box length.<br>
<br>
Question: how can I explain the difference? Does Gromacs have a different PME implementation than NAMD?<br>
<br>
P.S. my input scripts are in the attachments.<br>
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<br>
Steven W.<br>
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