[gmx-developers] ewald shift

Berk Hess hess at cbr.su.se
Fri Aug 28 11:23:14 CEST 2009

I looked at the Fennell paper and they use RF with charge groups.
I checked that when you use RF without charge groups
(coulombtype=reaction-field-zero in Gromacs)
it performs better than force shifted. This is to be expected, since RF
removes less of the force
than plainly shifting it with a constant.

But I would always use PME, especially for a crystal, since you really
have periodicity, right?


Harold Park wrote:
> Dear Berk:
> I'm not sure how well the Wolf methods work for liquid systems, though
> apparently there have been some tests to show that it works well.  I
> do not know enough to say much on this point.  We are looking at
> crystalline ionic solids, which is what the method was initially
> developed for.  Thanks for your suggestion for the shifted Coulomb
> option - we will explore this.
> Dear Rossen - I read the Fennell paper carefully, and the corrected
> form they utilize appears to be more robust and conserves force and
> energy at the cut-off - we will definitely implement their form
> instead.  Thank you very much for this reference!
> Regards to both of you,
> Harold
>> Message: 2
>> Date: Sat, 15 Aug 2009 21:18:27 +0200 (CEST)
>> From: hess at sbc.su.se <mailto:hess at sbc.su.se>
>> Subject: Re: [gmx-developers] ewald shift
>> To: "Discussion list for GROMACS development"
>> <gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org>>
>> Message-ID: <49431. at mail.sbc.su.se
>> <mailto:49431. at mail.sbc.su.se>>
>> Content-Type: text/plain;charset=iso-8859-1
>> Hi,
>> But that is what I meant.
>> A plain cut-off lead to serious artifacts,
>> at least for liquid systems. In water you get very strong dipole-dipole
>> anti-correlation/correlation at the cut-off radius. This effects
>> increases (!) with increasing cut-off distance.
>> My thesis has an example of this.
>> In liquid systems plain cut-off are almost not used anymore.
>> Referees will probably reject work done with a plain cut-off.
>> Reaction-field is better, but even that is mostly replaced by PME.
>> For something as rigid as a crystal it might work.
>> Shifted Coulomb is available in Gromacs with the mdp option
>> coulombtype = shift
>> Message: 3
>> Date: Sat, 15 Aug 2009 22:13:20 +0200
>> From: Rossen Apostolov <rossen at cbr.su.se <mailto:rossen at cbr.su.se>>
>> Subject: Re: [gmx-developers] ewald shift
>> To: Discussion list for GROMACS development
>> <gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org>>
>> Message-ID: <4A8716E0.2030701 at cbr.su.se
>> <mailto:4A8716E0.2030701 at cbr.su.se>>
>> Content-Type: text/plain; charset=ISO-8859-1
>> Hi,
>> You might want to check the Fennell potential method, which is an
>> extension of Wolf and improves the force discontinuity at cutoff:
>> Fennell, C. J.; Gezelter, J. D. J Chem Phys 2006, 124, 234104 and
>> Kikugawa et al., J Comput Chem. 2009 Jan 15;30(1):110-8.
>> Another alternative you might want to try is the isotropic periodic sum
>> method, Wu X, Brooks BR,  J Chem Phys. 2005 Jan 22;122(4):44107. You
>> should be careful though if you use it to simulate interfaces.
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