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

[Wang, Yuhang]

Dear Floris,

I actually did the FEP in steps: step 1, turn off electrostatics; step 2, turn off vdW. Parameters alchElecLambdaStart and alchvdWLambdaEnd were modified correspondingly. So that is not the problem. The real problem is I got two different results (~ 10kcal/mol difference) in step 1 (turning off electrostatics), although step 2 results matched quite well. Simulations in both packages used the same force field parameters for ion and water (TIP3P). PME was used in both cases. Then the question is why two packages differ from each other.


Steven W.
________________________________________
From: gmx-developers-bounces at gromacs.org [gmx-developers-bounces at gromacs.org] on behalf of Floris Buelens [floris_buelens at yahoo.com]
Sent: Monday, June 11, 2012 3:33 AM
To: Discussion list for GROMACS development
Subject: Re: [gmx-developers] issue on benchmarking FEP calculations in Gromacs and NAMD

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.

--
gmx-developers mailing list
gmx-developers at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-developers
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-developers-request at gromacs.org.
--
gmx-developers mailing list
gmx-developers at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-developers
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-developers-request at gromacs.org.