Dear users,
I am simulating a 22-mer DNA in a 15 ang box of TIP3P water.
I want to study the behaviour of this DNA under different salt
concentrations (100-400 mM).
I use the script provided by Prof. Cheatham to calculate the number of ions
to mimic the molarity for a given volume.
For net-neutralization of 22-mer DNA, I would require 21 Na+ ions.
For a 15 ang box, say for 200 mM, I need to add 30 Na+ and Cl- ions.
My question is, the 30 Na, Cl ions required for the 200mM will include the
net-neutralizing ions?
In my case, how many ions should I add?
21 (neutralizing Na+) + 30 (excess Na+) + 30 (excess Cl-)?
or
21 (neutralizing Na+) + 9 (excess Na+) + 9 (excess Cl-)?
It will be greatly helpful with suggestions in this regards.
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Received on Thu Dec 22 2016 - 05:30:03 PST
