Re: Accelerated MD documentation?

From: Chris Harrison (charris5_at_gmail.com)
Date: Sat Mar 19 2011 - 00:15:15 CDT

Dear Francesco,

The present accelerated MD in NAMD is Hamelberg-McCammon. The paper
you cited, I'll call it Hamelberg2011, describes the problem of
Hamelberg-McCammon to accurately reproduce the transition states (TS)
of the underlying "true" potential surface when the cutoff energy is
very large - cutoff energies, that as I interpreted, are larger than
the energies of the transition states/barrier regions. Hamelberg2011
goes on to demonstrate that accurate TS rates are obtained
with multiple accelerated MD simulations using different water models and
different values of alpha (at a constant E cutoff). Then using Kramer's
rate theory with the different alpha values and curvatures of the well
and barrier regions from unweighted free energy profiles, the accurate
transition rate/kinetics can be calculated for the barrier regions.
Noticing the diffusion coefficents didn't change significantly between
the water models, it was suggested that, instead of a series, one could
do a single accelerated MD and calculate the apparent diffusion
coefficient. Then plugging the diffusion coefficent, the curvatures of
the well and barrier, and the barrier height into Kramer's rate equation
yields kinetic values very similar to those obtained from the above
mentioned series of accelerated MD simulations. So Hamelberg2011 seems
more an approach to performing your accelerated MD and
post-processing with Kramer's theory (as proposed in J Chem Phys 132
224101) to tease out accurate kintetics from accelerated MD runs that
don't accurately characterize barrier regions.

And here's hoping I didn't mangle Donald Hamelberg's method in my
explanation. Does this help explain the relevance of the 2011 paper
from Hamelberg and coworkers to the current accelerated MD
implementation in NAMD?

Best,
Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 217-244-1733
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
Francesco Pietra <francesco.pietra_at_accademialucchese.it> writes:
> Date: Tue, 15 Mar 2011 16:20:18 +0100
> From: Francesco Pietra <francesco.pietra_at_accademialucchese.it>
> To: Chris Harrison <charris5_at_gmail.com>, NAMD <namd-l_at_ks.uiuc.edu>
> Subject: Re: namd-l: Accelerated MD documentation?
> 
> CHris:
> I had the opportunity in the recent past to use Hamelberg-McCammon
> accelerated MD thanks to the courtesy of Professor Donald Hamelberg. I
> tried to rectify a kicked helix. Now Professor Hamelberg seems to have
> fundamentally modified his algorithm, or taken another route to the
> task. I did not ask him, I simply came across "Extracting realistic
> kinetics of rare activated processes from accelerated MD using
> Kramers' theory" on a recent journal. being busy with a "constant pH"
> simulation, I paid only cursory attention so far to the paper, getting
> the impression that previous algorithm had its problems. Is present
> accelerated MD in NAMD the original Hamelberg-McCammon? Has anything
> to do with the article that I cited?
> thanks
> francesco pietra
> 
> On Tue, Mar 15, 2011 at 3:28 PM, Chris Harrison <charris5_at_gmail.com> wrote:
> > :) †Flattering that we have such careful attention paid to the nightly
> > code releases. †The accelerated MD documentation will be available in
> > the source in the next day or two. †Thanks for letting us know you're
> > interested to use it!
> >
> >
> > Best,
> > Chris
> >
> >
> > --
> > Chris Harrison, Ph.D.
> > Theoretical and Computational Biophysics Group
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> >
> > char_at_ks.uiuc.edu † † † † † † † † † † † † †Voice: 217-244-1733
> > http://www.ks.uiuc.edu/~char † † † † † † †Fax: † 217-244-6078
> >
> >
> > Bjoern Olausson <namdlist_at_googlemail.com> writes:
> >> Date: Tue, 15 Mar 2011 14:59:48 +0100
> >> From: Bjoern Olausson <namdlist_at_googlemail.com>
> >> To: namd-l_at_ks.uiuc.edu
> >> Subject: Re: namd-l: Accelerated MD documentation?
> >> Reply-To: namdlist_at_gmail.com
> >> User-Agent: KMail/1.13.5 (Linux/2.6.36.2-unpatched; KDE/4.4.5; x86_64; ; )
> >>
> >> On Tuesday 15 March 2011 14:05:19 you wrote:
> >> > I see that accelerated MD is now implemented in the "nightly build" version
> >> > of NAMD. Is there any documentation available describing the details of
> >> > how to invoke it from NAMD, what the parameter names are & etc.?
> >> >
> >> > Thanks.
> >> >
> >>
> >> I am also curious about the new options.
> >>
> >> http://www.ks.uiuc.edu/Research/namd/cvs/ug/node62.html
> >> only lists the same methods as in 2.7
> >>
> >>
> >> Cheers,
> >> Bjoern
> >>
> >> --
> >> Bjoern Olausson
> >> Martin-Luther-Universitšt Halle-Wittenberg
> >> Fachbereich Biochemie/Biotechnologie
> >> Kurt-Mothes-Str. 3
> >> 06120 Halle/Saale
> >>
> >> Phone: +49-345-55-24942
> >
> >
> >
> >

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