AMBER Archive (2008)

Subject: Re: AMBER: The forming of micelle

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Mon Sep 22 2008 - 14:02:30 CDT

Hi
My solute is not large, 33 atoms.....
Is it possible to form micelles using atomistic simulation of MD?

Thank you
Lin

----- Original Message -----
From: Adrian Roitberg <roitberg_at_qtp.ufl.edu>
Date: Monday, September 22, 2008 11:24 am
Subject: Re: AMBER: The forming of micelle
To: amber_at_scripps.edu

> 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
> >
> > ------------------------------------------------------------------
> -----
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" (in the *body* of the
> email)> to majordomo_at_scripps.edu
> >
>
> --
> 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
> --------------------------------------------------------------------
> ---
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu