[gmx-developers] Bug in Ewald Code?

[hessb at mpip-mainz.mpg.de]

> 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.