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

Erik Lindahl lindahl at sbc.su.se
Wed Mar 29 23:53:18 CEST 2006

Hi David,

We only want one default value for each parameter, so having special  
ones for free energy probably won't happen. Adding a warning might be  
an alternative, but before doing so we'll need to be sure it's really  
a fundemental limitation of the algorithm and not some artifact.

I assume that your values converge if you use even tighter limits  
(e.g. order 8 or spacing 0.8)?

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.



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
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