AMBER Archive (2008)

Subject: Re: AMBER: The forming of micelle

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Tue Sep 23 2008 - 19:07:47 CDT

Hi
Have anyone experienced the simulation of forming the micelles using Amber?

Thank you
Lin

----- Original Message -----
From: Chih-Ying Lin <chihying_at_usc.edu>
Date: Monday, September 22, 2008 12:26 pm
Subject: Re: AMBER: The forming of micelle
To: amber_at_scripps.edu

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