[gmx-developers] suggestion for PME for 3.3.1 for free_energy=yes
dmobley at gmail.com
Thu Mar 30 00:07:42 CEST 2006
> I assume that your values converge if you use even tighter limits
> (e.g. order 8 or spacing 0.8)?
It looked like it, although I must admit I didn't go to order 8, so
I'll start that running now (should be done tomorrow).
> However, instead of increasing the amount of PME work I would
> recommend checking what happens with longer direct-space cutoffs. The
> default PME values are pretty similar to Tom Darden's default ones,
> and since Gromacs is much faster on direct-space interactions than
> his code we should move more interactions there.
Benchmarking here and by Michael suggested it was cheaper to increase
the pme_order and fourier spacing than increase rcoulomb, although I
think Michael's suggestion would be to do both (rcoulomb>=1.0). I'm
going to start a couple runs going to check the case of rcoulomb
larger (1.0 or 1.1) but PME order 4 still with the 0.12 A spacing, as
well as rcoul=0.9 (my original) with order 8 and spacing 0.08. Let me
know if you'd like me to check other combinations, although not too
many (I run these for about a day on 5 processors each).
> On Mar 29, 2006, at 11:33 PM, David Mobley wrote:
> > Dear all,
> > I wanted to write and suggest that the default PME parameters be set
> > differently when free_energy=yes in the 3.3.1 release. In particular,
> > I think the default pme_order needs to be 6 with a fourier spacing of
> > 0.10 or better. ewald_rtol probably isn't as important but I would
> > suggest 1e-06.
> > Currently, in 3.3, the default pme_order=4 with ewald_rtol=1e-05 and
> > fourierspacing=0.12. Michael Shirts and I have done some testing (he
> > can comment on his testing separately if he likes) and found that with
> > pme_order=4, results for free energy calculations involving
> > modifications of electrostatics can be substantially wrong.
> > My particular testing has mostly been done with rcoulomb=1.0 or 0.9,
> > although Michael has looked more at varying this, as well. Regardless,
> > I find that results for computed free energies involving changes in
> > electrostatics can be wrong by 1-4 kcal/mol with the default pme
> > parameters as compared to their values with higher pme_order and lower
> > fourierspacing. For my own work I think I've ended up settling on
> > pme_order=6 and fourier_spacing=0.10 with ewald_rtol=1e-6, as my
> > results don't seem to change substantially if I further reduce
> > fourier_spacing or ewald_rtol, or even increase rcoulomb. Again,
> > though, I want to emphasize that the difference in free energies going
> > from the default PME parameters to the ones I suggest here is 1-4
> > kcal/mol (I tested this on some polar molecules including phenol; the
> > difference is smaller for less polar molecules), which is roughly
> > comparable to the total hydration free energy for such molecules.
> > If for some reason you decide it's not a good idea to change the
> > default PME parameters (at least for free_energy=yes), I would
> > strongly encourage adding some suitable warnings if free_energy=yes
> > with these parameters, and probably also in the documentation.
> > I can provide exact values for the computed free energies, etc. as
> > needed. It is possible of course that the *best* parameters for these
> > things are system-dependent, but it seems pretty clear that
> > pme_order=4 with fourier_spacing=0.12 is NOT adequate for free energy
> > calculations involving modification of charges, at least when the
> > charges are reasonably polar.
> > Thanks,
> > David Mobley
> > UCSF
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