AMBER Archive (2009)

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

From: Nicolas SAPAY (nicolas.sapay_at_cermav.cnrs.fr)
Date: Mon Nov 02 2009 - 08:19:17 CST

Hello Nicholus,

This is not that easy to answer to your question since the performance of
your calculation depends on many factors, including:
  - the number of processors you are using;
  - their frequency;
  - the hardware/software used by processors to communicate;
  - the number of particles in your system;
  - whether you are using PME or not;
  - ...

I made a test recently with a 30000 atoms system on a single Intel proc at
2.4 GHz (cutoff at 0.8 nm with PME). The OS was Fedora 10 and I used the
GNU compiler. I was able to compute 0.41 ns per day which is not
particularly great but sufficient to setup, minimize and equilibrate a
system (in bulk water).

Cheers,
Nicolas

> 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)
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
[ Nicolas Sapay - Post-Doctoral Fellow ]
CERMAV - www.cermav.cnrs.fr
BP53, 38041 Grenoble cedex 9, France
Phone: +33 (0)4 76 03 76 44/53

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