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

Floris Buelens floris_buelens at yahoo.com
Mon Jun 11 10:33:07 CEST 2012

I think you may be inadvertently coupling the van der Waals parameter of the ion to lambda in your NAMD configuration. Check in your trajectories whether you're seeing water overlap with the ion as you get to the end point, and read up on the values of alchVdwLambdaEnd and alchElecLambdaStart - the concept is a little different than for Gromacs, but I think what you need are values of alchVdwLambdaEnd=0 and alchElecLambdaStart = 0 to get the effect you're looking for (only decouple the electrostatic component without changing Lennard-Jones).

From: "Wang, Yuhang" <ywang148 at illinois.edu>
To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org> 
Sent: Friday, 8 June 2012, 18:21
Subject: [gmx-developers] issue on benchmarking FEP calculations in Gromacs and NAMD

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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