[gmx-users] Genion and number of Ions

Volker Knecht vknecht at gwdg.de
Wed Sep 25 15:28:57 CEST 2002

    Hello Marc,

> this might be a beginners question, but I have some problems with genion:
> I want to simulate a comparably large (~70 kDa) protein complex (three
> single protein molecules one ligand and some water in a solvent-environment.
> I did all steps as described in the tutorial: pdb2gmx, addition of the
> ligand-topology from PRODRG as described in the tutorial from John E.
> Kerrigan, solvation with editconf and genbox, compilation with grompp,
> addition of ions with genion.
> 1. Question: A friend of mine, who knows a bit more about MD-Simulation
> than I, told me to make a neutral setup i.e. add as many ions as
> necessary to bring the total charge to 0. Is there any other suggestion
> (at the moment I add only a few Na+-Ions, but this doesn't sound  too
> reasonable to me).

Alternatively, you could choose a physiological ion concentration.

> 2. Question: What to do with fractional charges (i.e. -3.2 ?)

You shouldn't have fractional charges. Although individual atoms of a molecule
may carry partial charges, the total charge of a molecule should be an integer.

Volker Knecht

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