[gmx-users] adding Ca2+ ions to the solvent (either randomly or restrained)

Mark Abraham Mark.Abraham at anu.edu.au
Tue Sep 13 01:27:19 CEST 2011

On 13/09/2011 12:03 AM, m r wrote:
>   Dear all,
> In an attempt to simulate the effect of adding calcium ion to the solvent
> around my protein of interest, I wonder how to add Ca2+ ions in the
> following cases (in GROMACS 4.5.4):
> 1) adding Ca2+ ions randomly distributed in the solvent;

genion does this

> 2) adding Ca2+ such that it is initially restrained in vicinity of some
> specified groups on the surface of my protein (I mean: something 
> similar to
> restraining the ligand in a search box during its docking to a receptor).

Nothing in GROMACS does this.

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