[AMBER] neutralization and Salt concentration for DNA simulations

From: Muthukumaran R <kumaran.bicpu.edu.in>
Date: Thu, 22 Dec 2016 18:55:18 +0530

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-)?
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
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