Francesco,
Take a look at the script in the AMBER tutorials that they use to run
20-1800ps of MD.
http://amber.scripps.edu/tutorials/basic/tutorial1/section6.htm Use
that script as a starting point. That script basically runs MD and
uses the last set of coordinates as the starting coordinates for the
next run. If you have any more questions please don't hesitate to
ask.
Seth
On 7/7/07, Francesco Pietra <chiendarret.yahoo.com> wrote:
> SetH:
> Did you get an answer to your "Currently my approach is to run several
> annealing runs consecutively using the last coordinates as the starting
> coordinates for the next run"of last May?
>
> I would be much interested in the script to perform that re-using of last
> coordinates, as a way to reach the global minimum (for natural products, not
> proteins or nucleic acids)
>
> Thanks
>
> francesco pietra
>
> >Subject: AMBER: Simulated Annealing - Best way to create randomness
> >From: Seth Lilavivat (sethl_at_gatech.edu)
> >Date: Fri May 04 2007 - 15:42:18 CDT
>
> * Previous message: Sean Rathlef: "Re: AMBER: Rate of Dissociation"
> * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
> >Dear Amber Users,
>
> >What is the best way to create different structures over the same annealing
> >algorithm? Is it unsual to start an annealing run with an initial temperature?
> > Currently my approach is to run several annealing runs consecutively using
> the
> >last coordinates as the starting coordinates for the next run.
>
> >Thanks,
> >Seth
>
>
>
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Received on Wed Jul 11 2007 - 06:07:26 PDT
