AMBER Archive (2001)

Subject: about ion concentration in protein simulation

From: Shixiang Yan (sy8_at_SCIRES.ACF.nyu.edu)
Date: Wed Jul 11 2001 - 08:48:16 CDT

i have a question about adding ions in simulating a large protein system.
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. 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. thanks for any
suggestions... frank