Re: about ion concentration in protein simulation

From: Bill Ross <ross_at_cgl.ucsf.edu>
Date: Wed 11 Jul 2001 15:49:27 -0700 (PDT)

        we were wondering if we only need the neutralizing ions, or if we can
        bring the ion concentration close to the physiological number which is
        about .15 M. i am wondering which solution would be better.

The trend these days seems to be to go with the physiological number.
I think it may have to do in part with easier equilibration.

        also because inside the cell most cations are K+ instead of Na+,
        is it better to add K+ than to add Na+, which we usually do in
        our simulation.

It can't hurt to use K+ - I would be mildly surprised if it made
any difference.

These questions are general enough to be worth asking on the chemistry
reflector.

Bill Ross
Received on Wed Jul 11 2001 - 15:49:27 PDT
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