[gmx-users] PME accuracy
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 7 16:45:01 CEST 2003
On Wed, 2003-05-07 at 15:47, Jason DeJoannis wrote:
> Hi gmx-users,
> Unfortunately, as I think it was David who pointed it
> out to me: there is no analytical error estimate for
> smooth PME yet. But as the error-estimates for Ewald, P3M
> and regular PME would suggest, the error varies with several
> things including the number of charges. Keep this in mind
> as well as the fact that the Ewald parameter is probably
> being adjusted "behind the scenes" in order to deliver
> the specified "ewald_rtol".
> If anyone knows of a way to find out what Ewald parameter
> (alpha) is being used, let me know. Also I am not very clear
> on what is being done, if anything, to the PME parameters
> behind the scenes. For example I have on occasion reduced the
> Fourier spacing to find no change was actually made in the
> mdout.mdp file. Is that possible? or am I mistaken?
If you also specify the grid points (nkx etc) that has prescendence over
the fourier spacing.
> best regards,
> Jason de Joannis, Ph.D.
> Chemistry Department, Emory University
> 1515 Pierce Dr. NE, Atlanta, GA 30322
> Phone: (404) 712-2983
> Email: jdejoan at emory.edu
> Quoting Vincent Ballenegger <vcb25 at cam.ac.uk>:
> > Dear gmx-users,
> > According to the gromacs manual, the PME method is such that "with a
> > grid spacing of 0.1nm and cubic interpolation (i.e. pme_order=4), the
> > electrostatic forces have an accuracy of 2-3e-4".
> > I did a small test and obtained the following results for the electric
> > force between two ions (charge +e and -e) a distance 2.35nm apart along
> > the diagonal of a cubic box of 3.5nm:
> > * Ewald method with fourier_nx=25:
> > force = -10.824 "exact result"
> > * PME method with fourier_spacing=0.1, pme_order=4:
> > force = -7.789 error: 28% !!!
> > * PME method with fourier_spacing=0.05, pme_order=4: (very slow!)
> > force = -10.932 error: 1%
> > * PME method with fourier_spacing=0.1, pme_order=6:
> > force = -10.716 error: 1%
> > Where is the claimed accuracy of 3e-4?
> > Thanks,
> > Vincent
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Dr. David van der Spoel, Dept. of Cell & Mol. Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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