Re: Simulation of Protein with Ions

From: Aron Broom (
Date: Wed Jul 03 2013 - 06:02:21 CDT

If you are wanting to have an ion in a specific binding site on the
protein, and you make the particular parameters for the ion bound residues
which have a fake bond to the ion (this is one of the recommended methods
of simulating ions in active sites for example) then this could still work
in implicit solvent. If on the other hand you want to have free ions
moving around, I don't think that is likely to work well.

If you just want to change the ionic strength because you are looking for
some general ionic strength effect, there is a parameter to do this.

On Wed, Jul 3, 2013 at 3:47 AM, Stephan Grein <> wrote:

> Hash: SHA1
> Dear NAMD users,
> is it possible to simulate a protein with ions but without explicit
> representation of water molecules? I've taken note about implicit
> water models in MD simulations - but can I do this?
> All the best,
> Stephan
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Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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