[gmx-users] charge_calculation

Mark Abraham mark.abraham at anu.edu.au
Fri Jul 27 01:41:55 CEST 2007

> I was wondering wether i should change the cgnr number to a
> single value or not since there is no charge neutrality
> within the individual groups after the substitution of the
> chelpg charges?

Larger, non-spherical charge groups will tend to create larger arithmetic
noise when calculating Coulomb contributions, because there will exist
atoms for which the group-based cut-off creates a region that is itself
not spherical.

> After calculation of charges i am getting a small residual
> charge of 3e-06 for my ligand. My ligand should be neutral.
> Is this small residual going to impact my simulations?

Probably not... but the charges you've calculated are so approximate
anyway, i.e. within the MM approximation, that you may as well round
something by 3e-06.

> Is there any other changes that i need to make while using
> these new charges?

I don't think so.


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