AMBER Archive (2005)

Subject: Re: AMBER: mm-pbsa with multiple-processors

From: Piotr Cieplak (cieplak_at_cgl.ucsf.edu)
Date: Mon Mar 21 2005 - 18:17:30 CST

The other solution is to design a command file that splits calculations
over the whole trajectory into its subsets and and perform subset processing
on each processor separately and then combine results.

Piotr

>Quoting Eric Hu <eric.y.hu_at_gmail.com>:
>
>> To my best knowledge, mm-pbsa uses single processor. Is there any work
>> done to take advantage of multiple-processors to speed up the
>> calculations (e.g. at least partially for sander)?
>
>I think you can modify the code by modifying the corresponding line for
>executing sander in parallel. I did it some times ago and it worked... It is
>unfortunately not possible for nmode since I think it does not work in
>parallel, regards,
>
> F.-Y. Dupradeau
>DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
>The Scripps Research Institute, La Jolla, CA, USA
> --
>http://www.u-picardie.fr/labo/lbpd/FyD.htm
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