[gmx-users] PME accuracy
jdejoan at emory.edu
Wed May 7 22:46:01 CEST 2003
I think you mean the other way around. In other
words alpha (the Ewald parameter) is chosen from:
ewald_rtol = erfc(alpha*rcoulomb)
The manual was kind of vague about that. For Ewald
simulations it would be more useful to select alpha from
the condition that the real-space and Fourier-space
have the same level of error... but as most people
use PME that's just a detail.
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 Erik Lindahl <lindahl at stanford.edu>:
> Hi Jason,
> The alpha parameter is calculated so that the "switched off" real-space
> interaction is PME_rtol fraction of the nonswitched interaction at the
> cutoff, just as it is in Tom Darden's original reference code.
> The fourierspacing value is the largest gridspacing you can tolerate.
> The actual grid used is calculated to optimize the dimensions for FFTW
> - you'll see a line about it when running grompp. In other words, if
> you only increase the gridspacing marginally it sounds quite normal
> that the actual grid dimensions didn't change.
> On Wednesday, May 7, 2003, at 06:47 America/Los_Angeles, 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?
> > best regards,
> > Jason
> > ---
> > 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
> > http://userwww.service.emory.edu/~jdejoan
> > 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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> Erik Lindahl, MSc, PhD <lindahl at stanford.edu>
> D109, Fairchild Building
> Dept. Structural Biology, Stanford University School of Medicine
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