AMBER Archive (2008)

Subject: Re: AMBER: The forming of micelle (CMC)

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Wed Sep 24 2008 - 17:00:45 CDT

Hi,

In principle, you would need to use in your simulation the same
concentration of solute as you would have in the real situation.

Have any of the papers you mention used real all atom simulations to
follow the micelle formation process? I did a quick search, and found
some articles that simulate micelle formation, but *all* of them use
some kind of simplified approach. OK, one of them (doi:
10.1529/biophysj.104.040279) is an actual all atom simulation, but
uses a very high concentration of solute molecules to force micelle
formation. Also, they use a limited time simulation because, at longer
times, "a catastrophic distortion of the micellar system may be
observed" (Humm....).

Here are some points for you to think about:

1. How many molecules of solute does it take to form one micelle?

2. Now, take this number, and put enough water around to get the
correct concentration you are interested in. How many atoms do you get
(total)?

3. Do some tests to see how long (in total wall time) does it take to
run a 1ns-long simulation with this many atoms.

4. Find out how long does it take *in the experiment* to form a
micelle. Basically, what is the physical timescale for the micelle
formation? As Adrian pointed out before, it would not be surprising if
it falls in the milisecond time scale.

6. Once you know the time you expect it to take (in ns), multiply by
the (wall)time it takes for you to simulate one ns. What do you get?
Is it a reasonable number?

What I believe you will get as a result is a number that is way beyond
the time you have available for you now, thus putting it "beyond
current capabilities", and all this is assuming that the force fields,
methods, etc. you choose are good enough in this time scale. (There
are examples of force fields working fine for small times, but
breaking down in very long simulations. See doi:
10.1529/biophysj.106.097782 for example.)

All this explains the need for methods to accelerate micelle
formation, such as unrealisticly high concentrations, or the use of
simplified methods such as coarse grained simulations.

HTH,
Gustavo.

On Wed, Sep 24, 2008 at 2:02 PM, Chih-Ying Lin wrote:
> Hi
> Usually, the CMC is low but good enough to form the micelle.
>
> I read some papers and people seem to start from a concentration much higher than CMC on their simulation.
>
> Could anyone have the idea about the starting concentration to form the micelles from simulation?
>
> Thank you
> Lin
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