[gmx-developers] Bug in Ewald Code?

Dave Rogers wantye at gmail.com
Wed Nov 1 17:53:41 CET 2006

> Message: 5
> Date: Wed, 1 Nov 2006 08:09:47 +0100 (CET)
> From: hessb at mpip-mainz.mpg.de
> Subject: Re: [gmx-developers] Bug in Ewald Code?
> To: "Discussion list for GROMACS development"
>         <gmx-developers at gromacs.org>
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>         <62322. at lnxsrv9.mpip-mainz.mpg.de>
> Content-Type: text/plain;charset=iso-8859-1
> > On Tue, 31 Oct 2006, Dave Rogers wrote:
> >
> >>Developers,
> >>
> >>Problem:
> >>  The ewald potential of the input configuration changes from
> >>sr=0.000000   recip=-0.094927 to sr=-460.603673 recip=-330.965952 for
> >>a single water molecule (all system files included below) when the
> >>bond type ([bonds] funct) is changed from 1 (default) to 6 (harmonic)
> >>for both of the bonds in Voth's water model!  For now I am unable to
> >>reproduce his numbers for that water model as he used a harmonic bond
> >>potential.
> >>
> >>Thanks for looking into this,
> >
> > please add exclusions manually and see if that resolves it. submit a
> > bugzilla anyway,
> This is exactly the reason for having the bond type 6.
> Type 1 and 6 are identical potentials, but type 6 does
> not produce a chemical bond and therefore no exclusions.
> Or is the problem that you do not want to use 1 because
> you want bond constraints for other molecules?
> Then you will indeed need to use 6 and you can add a chembond,
> bond type 5, to let Gromacs know that O should be chemically
> bonded to H. This will automatically generate the exclusions.
> Berk.


  You are right.  I am reading the version 3.3 manual, where section
5.3.5 mentions this.
  Unfortunately, I read through section 4.2 (Bonded interactions),
where the first potential mentioned is the "Harmonic Potential" and
the "Fourth Power Potential" contains a prescription for converting
stretch constants.  Next, I looked at table 5.4 and did not understand
the difference between bond types 1 and 6, except that 6 explicitly
says "Harmonic Potential".  Since I was having difficulty reproducing
the results I was after I tried bond type 6...
  It would have been helpful for me if table 5.4 included a reference
to the special role of bond types 6 and 7 and/or a reference to the
respective potential descriptions in sec. 4.2.  Hopefully changing
that will lower the number of misguided users such as myself.

David Rogers

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