It's the same thing as comparing molarity and molality. Either could be ok,
it depends on what you want.
On Jun 30, 2012 10:20 AM, "Anselm Horn" <Anselm.Horn.biochem.uni-erlangen.de>
wrote:
> Dear all,
>
> when looking through the posts about how to set up a defined salt
> concentration, a (maybe naive) question came into my mind:
>
> Is there a 'correct' volume reference for calculating the number of
> necessary ions?
>
> Of course, I'm aware of Prof. Cheatham's script that uses the complete
> volume of the simulation box. However, I also learned about an
> alternative approach where people use just the number of water molecules
> to compute the volume of this amount pure water and then add an
> appropriate number of ions.
>
> In the first case, one regards the simulation box as a complete solution
> unit, which seems justified to me especially for small solutes, i.e.
> Vol(solute)<< Vol(box)
> The second case treats the water/ion solution as reference to which the
> protein solute is then added.
>
> The difference in total added ions may be large for the two approaches
> when the protein system is big and occupies an significant fraction of
> the total simulation box.
>
> Thus, is there a 'standard' method for setting up the salt concentration?
>
> I'm looking forward to your comments!
>
> Regards,
>
> Anselm Horn
>
> Bioinformatik
> Institut für Biochemie
> Friedrich-Alexander-Universität Erlangen-Nürnberg
>
>
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Received on Sat Jun 30 2012 - 08:00:02 PDT
