[gmx-users] Parameters in PME

Janne Hirvi janne.hirvi at joensuu.fi
Tue Aug 2 11:46:20 CEST 2005


Hello!

I am not specially familiar with the deepest theory of PME, but I have tried to
figure out the meaning of all relevant electrostatics run parameters in
Gromacs.
However I haven't been able to find out how can I determine or discover
parameters similar to traditional Ewald summation given in all journals. I
think that all these parameters should be in usage also in PME excluding the
differences in reciprocal space (k-vectors and grid).

So I suppose that rcoulomb correspondes to the cut-off in real space, but what
is the cut-off in reciprocal space? Is it just this fourierspacing parameter
(or gridspacing) without any "real" cut-off?

Then there are these pme_order and ewald_rtol, which I suppose to affect to the
convergence, but how can I get the level of convergence with respect to a fully
converged Ewald sum? Do I need to simulate one with using as accurate
parameters (pme_order and ewald_rtol) as possible and then compare?

How about then something called the separation factor? Can someone tell me what
it is? I have tried to find it from the literature, but without any "luck".

So there is many hard questions for me and I hope some of you more experienced
users could help me to understand these things. Thanks for you all in advance.


Janne Hirvi

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Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
Tel: +358 13 2513326 & +358 50 3474223
E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
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