Re: [AMBER] Proplem about how to set substrate concentration

From: Sérgio Marques <>
Date: Wed, 28 Dec 2016 14:09:08 +0100

The concentration is the number of moles per volume, and therefore you only
need the number of substrate molecules and the cell volume. I suggest you
add to your system an estimated number of acetate molecules and run one
equilibration minimization-dynamics cycle, so you have the equilibrated
volume of your system (in A3). From this you can calculate the operating
acetate concentration, which can be iteratively corrected by changing the
number of ligands and/or the initial volume of your box.

I hope that helped.

Sérgio Marques, PhD

Marie Curie Fellow at:
*Loschmidt Laboratories*
Department of Experimental Biology
Faculty of Science, Masaryk University
Kamenice 5/A13, 625 00 Brno, Czech Republic

On 28 December 2016 at 08:38, Shanghaitech University WuMeng <> wrote:

> Dear All,
> I am working on channel protein which substrate is acetate. I want to
> add lots of acetates in my simulation system to see if the acetate could
> pass through the channel or not, maybe I need to set some acetate
> concentration in the water solvent, but I don't know how to to it. I have
> searched this problem on the internet, but the information is less.
> Any suggestions would be greatly appreciated.Thank You Very Much!
> Sincerely,
> Wu Meng
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Received on Wed Dec 28 2016 - 05:30:02 PST
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