Re: Accelerated MD documentation?

From: Francesco Pietra (francesco.pietra_at_accademialucchese.it)
Date: Tue Mar 15 2011 - 10:20:18 CDT

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-Universität Halle-Wittenberg
>> Fachbereich Biochemie/Biotechnologie
>> Kurt-Mothes-Str. 3
>> 06120 Halle/Saale
>>
>> Phone: +49-345-55-24942
>
>
>
>

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