AMBER Archive (2001)

Subject: Re: about ion concentration in protein simulation

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Jul 11 2001 - 17:49:27 CDT

        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