AMBER Archive (2009)

Subject: Re: [AMBER] Is it taking too much time

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Mon Nov 02 2009 - 02:37:28 CST

On Mon, Nov 2, 2009 at 1:01 PM, manoj singh <mks.amber_at_gmail.com> wrote:

> You can do a quick benchmarking for your system by running few ps
> simulations. The simulation time is proportional to the length of the
> simulation.
>
> On Mon, Nov 2, 2009 at 1:08 AM, nicholus bhattacharjee <
> nicholusbhattacharjee_at_gmail.com> wrote:
>
> > Dear community,
> > I am running a protein simulation in my IBM 3400
> > server (specification
> > http://www-07.ibm.com/systems/in/x/hardware/tower/x3400/specs.html) with
> > AMBER 9. My protein is 50 amino acid long. I am doing an explicit solvent
> > simulation. Can anybody suggest what is the maximum time needed for this
> > simulation.
> >
> > --
> > Nicholus Bhattacharjee
> > PhD Scholar
> > Department of Chemistry
> > University of Delhi
> > Delhi-110007 (INDIA)
> > Phone: 9873098743(M)
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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My machine is taking 1/2 hour for 10 ps simulation. Is this very long? 

-- 
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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