[gmx-users] Fwd: FW: PME settings in free energy calculations

Dries Van Rompaey dries.vanrompaey at gmail.com
Tue Feb 9 15:11:35 CET 2016

Hi Mark,

Thanks for your pointers. The energies obtained with a shifted potential
match up a lot better.

Kind regards


On 9 February 2016 at 14:30, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
> On Tue, Feb 9, 2016 at 1:30 PM Dries Van Rompaey <
> dries.vanrompaey at gmail.com>
> wrote:
> > Hi,
> >
> > I'm not deliberately triggering the generic kernel.
> OK, well that means its a setup that we have deliberately not tried to make
> fast in the group scheme, because it's too hard to do for the expected
> usefulness.
> > I unfortunately have no
> > idea what's causing that. I uploaded logfiles for a setup with matching
> > cutoffs as setup3alt and setup2alt (I got quite a lot of warnings for
> this
> > setup, which is why I initially changed the cutoffs slightly).
> >
> > I'm a bit baffled what could cause the large difference between the
> verlet
> > setup with long cutoffs and the verlet setup with shorter cutoffs and
> PME..
> > After all, that's the one that should be fairly close in order to prove
> my
> > electrostatics treatment is appropriate. This difference seems to be a
> lot
> > more pronounced than the difference to the group scheme.
> >
> That's the easy one. You're comparing potentials from Verlet PME with a
> short-ranged potential shift with Verlet plain cutoffs with no potential
> shift. The shift is quite small with PME (that's what ewald-rtol is all
> about) but it applies to every single in-range interaction. Your
> long-cutoff calculation has a cutoff that is only ~3 times longer than the
> modified short-ranged form you used with PME. That increase in range is not
> going to get down to 1e-5 relative error from truncation at the cutoff, and
> it also applies to a lot more interactions. I expect that this is
> confounding all your comparisons with Verlet+PME - you need to compare with
> a scheme with a potential shift. (This also leads people astray when they
> are e.g. comparing total energies between GROMACS and codes that don't use
> the potential shift.)
> Whether such comparisons as alchemistry.org suggests worked reasonably
> well
> with Group+PME vs Group+long-cutoff (because neither used a potential
> shift) with current or old code, I don't know.
> Mark
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