Re: Simulation of a protein and calcium ions

From: Axel Kohlmeyer (
Date: Tue Oct 08 2013 - 03:29:40 CDT

On Tue, Oct 8, 2013 at 10:15 AM, Stephan Matthias Grein
<> wrote:
> Hash: SHA1
> Dear NAMD users,
> after a couple of weeks learning the NAMD/VMD basics, i came up with
> one question i could not figure myself:
> I have generated PSF/PDB files for my protein of interest, using
> consistent topoplogy and force field parameter files and a consistent
> NAMD script setup. Solvated this in a waterbox with PBC according to
> the manual - which works fine.
> I'm now interested in observing ions moving into binding pockets of
> the protein (which are reported by literature to be between some EC
> domains of the protein)... for that i solvated my protein with various
> concentrations using the AutoSolvation tool in VMD.
> However, at neither a low nor an extraordinary (unphysiologically)
> high ion concentration, i could observe ions moving into the binding
> pockets of the protein and which should stay there, according to
> literature, at least if the ion concentration is very high.
> Is there a general failure with my procedure? If yes, would you mind
> to point it out?

have you considered the time scale on which an ion would move in a
binding pocket?
have you considered that there is a energetic component (you may have
to cross energy barriers), but also a statistical component (the ion
has to "find" the path towards the binding site)?


> Thanks in advance,
> Stephan
> - --
> M. Sc. Stephan Grein
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> =K6jY

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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