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

[Dawid das]

Thank you, now I understand relationship between beta and ewald_rtol :).
I will read the article you suggested and let you know if I have further
questions.

2017-01-02 19:00 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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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