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 - 07:30:02 PDT
