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

Roland Schulz roland at utk.edu
Mon Jun 11 05:34:46 CEST 2012

On Fri, Jun 8, 2012 at 12:21 PM, Wang, Yuhang <ywang148 at illinois.edu> wrote:

>  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?
Since you are using PME (and not PME-Switch) you don't have a buffer
region. That is different from NAMD. So if you want to make sure that this
isn't the cause of the difference you might want to check Gromacs with
PME-Switch. If you don't mind pre-release code you can also try out pre-4.6
and verlet-PME that is even closer to how it is in NAMD:

PS: Please send user questions to gmx-users not gmx-developers.


> P.S. my input scripts are in the attachments.
> Steven W.

ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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