AMBER Archive (2008)

Subject: Re: AMBER: The forming of micelle

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Mon Sep 22 2008 - 13:20:50 CDT

I might be talking outside my expertise here.
But..
Have you EVER seen or read about an atomisticsimulation forming a
micelle spontaneously ?
DO not think so....
Before someone flames me, of course there are simulations out there that
do this, but they are done with coarse grained models, which allow for
two things:
1. reduce substantially the number of atoms
2. increase substantially the time steps you can do.

Going back to the question, I would not be surprised if forming a
micelle with all atoms requires simulation time of a millisecond or so,
clearly beyond current capabilities.

Adrian

Chih-Ying Lin wrote:
>
>
> Hi
> I heard that it takes very long to see a micelle forming.
> How long should be the simulation time to see the micelle forming?
> How many nanoseconds to put on the simulation?
>
>
> Is there any particular difference to simulate the micelles than the tutorials described?
> My simulation steps are
> 1. prepare the topology files and coordinate files for the water and the solute
> 2. generate the simulation box / put water and solute together
> 3. do the minimisation
> 4. run MD with longer simulation time
>
> Thank you
> Lin
>
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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