[gmx-users] Should I keep the total charge unchanged?

[David Mobley]

If you are using long range periodic electrostatics like PME, etc., you need
to have a neutral system to avoid getting infinite energies, hence you need
to maintain a neutral system by changing the number of counterions. It's not
clear to me what this means for your energies. And if you're comparing the
absolute energies you compute with MD for the two systems, you probably
should be aware that these values typically have very large variances
compared to any difference in energy, so the sort of comparison you're
looking for may be difficult. Plus binding is really determined by the
binding free energy, which is somewhat more difficult to compute than simply
the enthalpy of the system.

Someone else may be better able to comment on how to do what you're trying
to do, as I'm not too sure.

Best wishes,
David Mobley

On 1/4/06, Mikko Hellgren <Mikko.Hellgren at mbb.ki.se> wrote:
>
> Hi Gromacs Users!
>
> I am doing simulations on a small peptide and looking at the binding
> of zinc to cys. When I change the protonation of the cys (0 to -1),
> should I counterbalance this charge with one less Cl- atom to get a
> neutral system, and if so why? If I compare energies between different
> protonation states, how should I handle this change in the system
> (with a different amount of Cl-)?
>
> Many thanks in advance
> Mikko Hellgren, Graduate Student at Karolinska Institutet in Sweden
>
>
>
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