Re: [AMBER] Adenine in water

From: Jason Swails <>
Date: Sun, 21 Mar 2010 02:41:35 -0400

On Fri, Mar 19, 2010 at 9:42 AM, ros <> wrote:
> Hello Amber users!
> I am trying to simulate the interactions of adenine in water but I dont know
> how to set up the constant volume (NVT ? NTB=1?) conditions so the
> simulation does not "dilute" in space.  How can I set up a box of, for

Not quite sure what you mean here... NVT is simulated by setting
ntb=1. Particles do diffuse out of the periodic box (but then they
diffuse into the other side of the periodic box, since technically an
infinite number of systems are being simulated). NVT simply means
that the dimensions of the periodic box won't be changing (and your
concentration will remain constant). It seems fairly straightforward
to calculate an experimental concentration-- just find the volume of
your box and the number of moles of solute you have (moles / volume).

Also, rather than putting multiple solvent particles in a 15x15 box to
increase the concentration, I would probably just shrink the box
(unless of course there are reasons that you can't/don't want to).
You can also use "combine" in leap to add more copies of a pdb
structure to a unit without needing to add another copy to your PDB.
It may be helpful to use xleap here so you can visualize the system
and move them away from one another if you do make copies. You can
find good documentation of these features in the ambertools manual.

> example 15x15x15 A so the sim takes place in there?

quick math: 15x15x15 Angstrom is 15 x 15 x 15 = 3375, angstrom ^ 3 is
10^-9 dm ^3, which is 3.375 x 10 ^ -24 L. Putting one particle in
that box gives a concentration of about 0.5 M. Two particles would
double that concentration.

> What is the correct number of molecules to put in a simulation like this?
> For example, I know that in a NMR study, they use concentrations in the
> order of pico-moles.   If you have a box of 15x15x15 A, how many molecules
> you have to put in the initial PDB file?

Simulating true picomolar concentrations would require too large of a
box for most systems. Simulating 1 particle, it would have to be in a
volume 1.66 x 10 ^ -15 L, which is equivalent to about a 10^-5
dm-length box, which is like a 10000x10000x10000 angstrom box. This
is not something you ever see done.

Hope this helps,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Sun Mar 21 2010 - 00:00:03 PDT
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