Dear Dan,
Thank you for two references. I will read both.
Wu
-----Original Message-----
From: Daniel Sindhikara [mailto:sindhikara.gmail.com]
Sent: Wednesday, September 07, 2011 11:13 PM
To: AMBER Mailing List
Subject: Re: [AMBER] results from independent simulations
I guess I should chime in here.
Chaotic motion of proteins/peptides was shown by Braxenthaler et al:
Braxenthaler, M.; Unger, R.; Auerbach, D.; Given, J. A.; Moult, J. Chaos
in
protein dynamics. Proteins: Struct., Funct., Genet. 1997, 29 (4), 417-425.
I wrote a paper on the use of different random seeds and the problem that
two independent runs from different initial conditions they can look
similar
if you use the same random seed. This is essentially the opposite of chaos
(a negative lyapunov exponent):
D. Sindhikara, S. Kim, A.F. Voter, A. Roitberg, J. Chem. Theory Comput. 5,
1624 (2009)
Specifying different random seeds is easy to do in amber via the ig flag.
-Dan
On Thu, Sep 8, 2011 at 1:02 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, Sep 7, 2011 at 5:58 AM, Simon Becker
> <simon.becker.uni-konstanz.de>wrote:
>
> >
> > .jason: the shaw group: what are you referring to? is there a
> > publication I missed (again)? please let me know.
> >
>
> DESRES, Anton, desmond (milli-second long simulations):
> http://www.deshawresearch.com/ (they have publications there). It's
neat
> to
> see what you can do with lots of $$ and a diverse team of hardware and
> software experts -- they designed an MD-supercomputer running its MD
code
> with simulation times exceeding 1 ms for some systems.
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Thu Sep 08 2011 - 05:30:04 PDT
