On Thu, Feb 7, 2013 at 3:23 AM, Indrajit Deb <biky2004indra.gmail.com>wrote:
> Dear Amber Users,
>
> I have a small nucleic acid system that I want to simulate.
>
> 1 mM of this system is in 0.7 ml 25 mM phosphate buffer, pH 7.0, containing
> 25 mM NaCl, 10 mM MgCl2 and 0.2 mM EDTA for NMR study.
>
> I want to prepare same experimental setup for my system.
>
It's highly unlikely you will be able to do this. For example, I recently
calculated the ionic strength of one of my simulations where I added a 10
Angstrom solvent buffer around a 130-residue protein, after which I added
15 Cl- and 6 Na+ total ions (the protein was +9). The resulting
concentration was 200 mM. If I had added just 1 Na+ and 1 Cl- ion, the
concentraton would've still been ~20 mM (and I would not have been able to
neutralize my system).
In order to simulate such small concentrations of so many compounds, you
would need an incredibly large volume with a very large number of water
molecules. And to make matters worse, there are no good parameters for
magnesium ions.
Before running these simulations, you really should have a well-formed
question that you want to ask with a hypothesis about what you think will
happen. This is what you should use to design your experiment -- it is
unlikely that everything in your solution will be necessary to gain insight
from computation.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Feb 07 2013 - 07:00:02 PST
