Hello!
You will first use the necessary ions to neutralize your system, in tleap
you can use:
addions dna Na+ 0
addions dna Cl- 0
This will add the required ions to reach a final charge of 0. Then, add an
excess of ions to reach your desired concentration:
addions dna Na+ 30
addions dna Cl- 30
Hope that helps!
Rodrigo.
On Thu, Dec 22, 2016 at 6:25 AM, Muthukumaran R <kumaran.bicpu.edu.in>
wrote:
> 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 - 08:30:03 PST
