As in any experiment, ideally you'd have several different independent
runs (by changing the initial random number seed, initial coordinates,
or other conditions) to support a conclusion.
Unless you are running on a single CPU core using the same random number
seed, you'll not get exactly the same results in 2 MD runs (the numbers
will not be the same) .. However, you should be able to support a
finding that you want to report with more than a single simulation . On
the other hand, if you have experimental data to compare with and if you
run 1 simulation which agrees perfectly with experiment, it might be
enough. Although personally, I am not very supportive for drawing
conclusions from a single simulation, regardless of the agreement with
experiment.
Best wishes
Vlad
On 05/18/2013 12:19 PM, Kanin Wichapong wrote:
> Dear Amber Users,
>
> I have just some general questions about performing MD simulations?
>
> Do we really need to repeat the MD run? And when you repeat the MD runs do
> you get the same results?
>
>
> Best Regards,
> Kanin
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--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Sat May 18 2013 - 05:00:03 PDT
