[gmx-users] How the default parameters for PME (particle mesh Ewald) are chosen?

[Mark Abraham]

Hi,

On Mon, Jan 2, 2017 at 6:31 PM Dawid das <addiw7 at googlemail.com> wrote:

> I went through this manual before posting these questions,


Great, but it would have been more efficient to mention what you did find,
rather than that you didn't find anything :-)


> and I'm sorry if
> I'm to blind to see that but
> I don't understand how they would answer my questions. Could you give me a
> clearer explanation, please?
>

beta is defined in the reference manual section for Ewald, e.g. 4.8 in the
2016 version. From the equations there, and the fact that ewald_rtol is a
relative strength, it follows that

ewald_rtol = erfc(beta * rcoulomb)

Merely varying beta without considering how the value of rcoulomb interacts
with it to affect the relative strength of the two components would be an
oversimplification. See also
http://onlinelibrary.wiley.com/doi/10.1002/jcc.21773/full (shameless self
plug). With ewald_rtol constant, you can scale rcoulomb and fourierspacing
by the same factor and get an approximately equivalently accurate PME model
(which mdrun -tunepme does).

If you don't understand the documentation for fourierspacing, please
suggest what aspect is the problem.

Mark


> Dawid
>
> 2017-01-02 18:19 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
> > On Mon, Jan 2, 2017 at 3:46 PM Dawid das <addiw7 at googlemail.com> wrote:
> >
> > > Dear All,
> > >
> > > I have at least two questions regarding PME in Gromacs 5.0.4.
> > >
> > > Firstly, in my *.log file there is a line that reads
> > >
> > > Will do ordinary reciprocal space Ewald sum.
> > > Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
> > >
> > > Is "beta" the relative weight of direct and reciprocal sums? If this is
> > the
> > > default value,
> > > how to control this parameter?
> > >
> >
> > No. See ewald-rtol at
> > http://manual.gromacs.org/documentation/2016/user-guide/
> > mdp-options.html#ewald
> >
> >
> > >
> > > Secondly, for all my calculations I do not specify
> > >
> > > fourier-nx, -ny and -nz
> > >
> > > parameters. On what basis are they chosen to be default?
> > >
> >
> > See above link.
> >
> > Mark
> >
> >
> > > I could not find answers to these questions in the manual.
> > >
> > > Best regards,
> > > Dawid Grabarek
> > > --
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