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

Wang, Yuhang ywang148 at illinois.edu
Tue Jun 12 00:45:23 CEST 2012

Dear Igor,

Both FEP simulations I did were done using slow growth method (20 windows). I agree with what you said: GROMACS needs correction. But, I just found out that NAMD doesn't need correction, because I set "alchDecouple=on", so that the self interaction term is always there (regardless of change in lambda). That's why two softwares produced different results. With that taken into account, there electrostatic desolvation free energy of SOD is ~ 82 kcal/mol in both cases.

Steven W.
From: gmx-developers-bounces at gromacs.org [gmx-developers-bounces at gromacs.org] on behalf of Igor Leontyev [ileontyev at ucdavis.edu]
Sent: Monday, June 11, 2012 4:51 PM
To: gmx-developers at gromacs.org
Subject: [gmx-developers] Re: issue on benchmarking FEP calculations in Gromacs and NAMD

Recently I did FEP calculations for Na+ by Gromacs and Amber packages and
found excellent agreement. Please, make sure that there is no miscounting of
the Ewald correction in your data because the results suspiciously differ by
the exact value of the correction (~11.5 Kcal/mol). As I know Gromacs and
other common codes do not include the correction in their output. Aslo try
to recalculate free energy by simple slow growth method: init_lambda=0;

Igor Leontyev

> Hi,
> What is the correction you applied?
This is Ewald correction suggested by G. Hummer and co-authors J. Phys.
Chem. 1996, 100, 1206 to extract from output the interaction  energy of the
solute with own periodic images. This is necessary to compare the simulation
with periodic boundary conditions (in which the solute interacts with
itself) with experimental data corresponding to infintly deluted solutions.

> I think Gromacs has all charge corrections in, except for the set of
> corrections
> required for absolute solvation free energies as described by Philippe
> Hünenberger.

The Ewald correction is not applied in Gromacs. Otherwise, the charging
energy of ion in empty box (no solvent) would be zero which is not true.

> Cheers,
> Berk

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

More information about the gromacs.org_gmx-developers mailing list