[gmx-developers] suggestion for PME for 3.3.1 for free_energy=yes

[David Mobley]

Erik,

These are in dodecahedral boxes. So far I prefer them because they
save some water molecules for things that are fairly spherical,
although if there is some technical reason these might be worse, I am
happy to switch.

Thanks,
David

On 3/29/06, Erik Lindahl <lindahl at sbc.su.se> wrote:
> Hi David,
>
> Great. Right now 3.3.1 is our priority, but then I'll write some code
> to actually check the dG/dl values in the PME routine.
>
> One more thing - are you using rectangular or triclinic (truncated
> octahedron/rhombic dodecahedron) boxes?
>
> Cheers,
>
> Erik
>
> On Mar 30, 2006, at 12:07 AM, David Mobley wrote:
>
> > Erik,
> >
> >> 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).
> >
> > Thanks,
> > David
> >
> >>
> >> Cheers,
> >>
> >> Erik
> >>
> >> 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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