[gmx-users] how to simulate 2 structures together

Tue Apr 1 12:51:10 CEST 2008

Hiiiiii
I want to simmulate and minimize two protein structures together in water,
can you tell me  any tutorial online or send me any information.

Radhika

On 4/1/08, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
wrote:
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> Today's Topics:
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>    1. RE: Blue Gene/P (Berk Hess)
>    2. Re: Blue Gene/P (Hannes Loeffler)
>
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 1 Apr 2008 09:34:54 +0200
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] Blue Gene/P
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BLU134-W34F03667F04F0F007F19798EF50 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> Gromacs 4 has blue gene optimized inner loops, which give a factor of 2
> performance improvement.
> On a BG/L it runs at 20-25% of the speed of x86 cores, but it scales
> quite well.
>
> Berk.
>
>
> > Date: Mon, 31 Mar 2008 17:29:57 -0700
> > From: tieleman at ucalgary.ca
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Blue Gene/P
> >
> > Thanks. I've seen the BG/L argument, but BG/P processors are faster. I
> > have no idea how much though, and am looking for actual numbers or if
> > those are not available a guess based on actual BG/L numbers and some
> > argument about scaling to a BG/P.
> >
> > Cheers,
> > Peter
> >
> > Mark Abraham wrote:
> > > Peter Tieleman wrote:
> > >> Hi,
> > >>
> > >> Has anyone run benchmarks on a BlueGene/P ?
> > >
> > > The word from IBM in December was that since GROMACS 3.x would lack
> > > both assembly inner-loops and threading on BlueGene/L, that it wasn't
> > > worthwhile running GROMACS on onw. I figure that goes for BlueGene/P
> too.
> > >
> > > Mark
> > > _______________________________________________
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> ------------------------------
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> Message: 2
> Date: Tue, 01 Apr 2008 09:10:09 +0100
> From: Hannes Loeffler <h.loeffler at dl.ac.uk>
> Subject: Re: [gmx-users] Blue Gene/P
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1207037409.5122.14.camel at zgb83773vig.dl.ac.uk>
> Content-Type: text/plain
>
> Ok, here just a few numbers.
>
> System: 52.000 atoms, coarse-grained, 500.000 steps
>
> BlueGene/P: 16(procs) x 4(threads) = 64 tasks (or whatever they are
> called)
>    8x4   7.25 h
>   16x4  11    h
>   32x4  > 12  h (queue only allows <= 12 h)
>
> BlueGene/L:
>   16x2  10 h
>   64x2  > 12 h
>
> Note: the procs x threads figures above are the numbers I asked for.  It
> may be possible that the scheduler distributes in a different manner.  I
> don't now.
>
> That's all I have for the moment.
>
>
> On Mon, 2008-03-31 at 17:29 -0700, Peter Tieleman wrote:
> > Thanks. I've seen the BG/L argument, but BG/P processors are faster. I
> > have no idea how much though, and am looking for actual numbers or if
> > those are not available a guess based on actual BG/L numbers and some
> > argument about scaling to a BG/P.
> >
> > Cheers,
> > Peter
> >
> > Mark Abraham wrote:
> > > Peter Tieleman wrote:
> > >> Hi,
> > >>
> > >> Has anyone run benchmarks on a BlueGene/P ?
> > >
> > > The word from IBM in December was that since GROMACS 3.x would lack
> > > both assembly inner-loops and threading on BlueGene/L, that it wasn't
> > > worthwhile running GROMACS on onw. I figure that goes for BlueGene/P
> too.
> > >
> > > Mark
> > > _______________________________________________
> > > gmx-users mailing list    gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> > > posting!
> > > Please don't post (un)subscribe requests to the list. Use the www
> > > interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > >
> >
> > _______________________________________________
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> End of gmx-users Digest, Vol 48, Issue 2
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