AMBER Archive (2002)

Subject: NaCl concentration

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Tue Apr 30 2002 - 14:34:38 CDT

Amber users:

I would like to run a DNA at 1 M NaCl and I am trying to decide how many Na+ and Cl- to add. I have taken the seemingly simple minded approach - I want 1 M NaCl, water is roughly 55.5 M, and my system has 2100 waters. Since the ratio of NaCl/water = 1/55.5, this gives 38 NaCl. But, since 10 Na+ are needed for the DNA phosphates, I've added 28 NaCl.

Is this a reasonable approach?

Thanks.

Pete