[gmx-users] NS in PME

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 4 15:45:10 CEST 2006

Janne Hirvi wrote:
> Hello David!
> I read your interesting new article "The Origin of Layer Structure Artifacts in
> Simulations of Liquid Water" and I would like to know especially what kind of
> NS parameters you have used in the simulations with PME and are the following
> parameters correct otherwise?
> dt=0.002
> nstlist=5
> rlist=?
> coulombtype=PME
> rcoulomb=0.9
> vdwtype=cut-off
> rvdw=?    
I'm attaching my mdp file.

We have just disabled the option to have rlist != rcoulomb with PME.

> I am interested especially about the rlist parameter because there seems to be
> some energy conservation problems in my water simulations. At least I couldn't
> achieve energy conservation with single precision complilation and with
> double precision compilation energy is conserved only when switch(shift?)
> function is used for vdw interactions (rlist>rvdw>rvdw_switch) and PME for
> coulombic interactions (rlist>rcoulomb). If rlist is equal to rcoulomb I need
> to update NS list at every time step but with preceding parameters energy is
> conserved even when nstlist=10. 
> So should I use rlist>rcoulomb with PME when nstlist>1 to take into account
> movement of atoms/molecules(charge groups) near the real space cut-off limit
> (rcoulomb) or is there something I don't understand? Atleast from the manual
> someone could get the picture that rlist should be equal to rcoulomb and there
> are also different kind of opinions on mailing list?

Maybe Berk can comment?

> Thanks for any comments in advance! 
> Janne
> ------------------------------------------------------------------------------
> Janne Hirvi, MSc(Physical Chemistry), Researcher
> University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
> Tel: +358 13 2514544 & +358 50 3474223
> E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
> ------------------------------------------------------------------------------
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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://folding.bmc.uu.se
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