AMBER Archive (2009)

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

From: manoj singh (mks.amber_at_gmail.com)
Date: Mon Nov 02 2009 - 07:50:21 CST

How many atoms are in your system, and what is the detail of the cutoff you
are using.

On Mon, Nov 2, 2009 at 3:37 AM, nicholus bhattacharjee <
nicholusbhattacharjee_at_gmail.com> wrote:

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