On Fri, Jun 8, 2012 at 12:21 PM, Wang, Yuhang <[email protected]> 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: http://lists.gromacs.org/pipermail/gmx-developers/2012-March/005674.html PS: Please send user questions to gmx-users not gmx-developers. Roland > > 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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