AMBER Archive (2007)

Subject: Re: AMBER: MDGRAPE and AMBER

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Feb 19 2007 - 08:23:58 CST


make sure that it supports the simulation methods that you want to use. this
means if you want to use PME, then compare benchmarks on the amber site to
those obtained using PME with the grape machine. Also check to see what is
involved when new version of amber come out- will the grape system work
right away, or does someone need to change the code? md-grape systems can be
very fast but sometimes the benchmarks compare things like simulations with
no cutoff, which nobody really uses.

On 2/19/07, Craig Gough <cgough_at_jbirc.aist.go.jp> wrote:
>
> Hello,
>
>
>
> I'm considering purchasing an MDGRAPE system for running AMBER (currently
> have AMBER 8 and 7 and may purchase AMBER 9 soon), and am curious about
> other researchers' experiences with this system. Can anyone enlighten me
> beyond what I can find on the amber.scripps.edu site (there doesn't seem
> to be much in the archive of this mail reflector).
>
>
>
> Much thanks in advance,
>
> Craig Gough
>
>
>
> *****************************************
>
> Craig Gough
>
> Integrated Database Team
>
> Japan Biological Information Research Center (JBIRC)
>
> AIST Waterfront Bio-IT Research Building, 7th Floor
>
> Aomi 2-42, Koto-ku, Tokyo
>
> 135-0064
>
> Tel: 03-3599-8810
>
> *****************************************
>
>
>

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