[gmx-users] how to simulate 2 structures together

Tue Apr 1 13:35:36 CEST 2008

Quoting Radhika Jaswal <jr7biophys at gmail.com>:

> 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.

I would suggest starting with basic tutorial material regarding simple
protein-in-water systems.  That way, you can gain appreciation for how to set
up a generic system within Gromacs, as well as understanding the topology
format.  Once you feel comfortable using the basic tools to set up a basic
system, then move on to a two-component system.  There are relevant discussions
in the list archive on how to deal with peptides with two chains, multiple
proteins, and so forth.  Do a thorough search of the archive, and post specific
questions when they arise.

-Justin

>
> 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:
> >
> >    1. RE: Blue Gene/P (Berk Hess)
> >    2. Re: Blue Gene/P (Hannes Loeffler)
> >
> >
> > ----------------------------------------------------------------------
> >
> > 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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> > ------------------------------
> >
> > 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
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> > > >
> > >
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> > End of gmx-users Digest, Vol 48, Issue 2
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> >
>

========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================