[gmx-users] Parameters in PME

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 2 14:26:33 CEST 2005

On Tue, 2005-08-02 at 12:46 +0300, Janne Hirvi wrote:
> 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?
Please read the Essman et al. paper, it is quite clearly written.
Reciprocal cut-off follows from number of grid cells IIRC.

> 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
> ------------------------------------------------------------------------------
> 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
> ------------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list