Hiiiiii<br>
I want to simmulate and minimize two protein structures together in
water, can you tell me any tutorial online or send me any
information.<br>
<br>
Radhika<br><br><div><span class="gmail_quote">On 4/1/08, <b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<br> When replying, please edit your Subject line so it is more specific<br> than "Re: Contents of gmx-users digest..."<br> <br> <br> Today's Topics:<br> <br> 1. RE: Blue Gene/P (Berk Hess)<br> 2. Re: Blue Gene/P (Hannes Loeffler)<br>
<br> <br> ----------------------------------------------------------------------<br> <br> Message: 1<br> Date: Tue, 1 Apr 2008 09:34:54 +0200<br> From: Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>><br>
Subject: RE: [gmx-users] Blue Gene/P<br> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Message-ID: <<a href="mailto:BLU134-W34F03667F04F0F007F19798EF50@phx.gbl">BLU134-W34F03667F04F0F007F19798EF50@phx.gbl</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br> <br> Hi,<br> <br> Gromacs 4 has blue gene optimized inner loops, which give a factor of 2<br> performance improvement.<br> On a BG/L it runs at 20-25% of the speed of x86 cores, but it scales<br>
quite well.<br> <br> Berk.<br> <br> <br> > Date: Mon, 31 Mar 2008 17:29:57 -0700<br> > From: <a href="mailto:tieleman@ucalgary.ca">tieleman@ucalgary.ca</a><br> > To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Subject: Re: [gmx-users] Blue Gene/P<br> ><br> > Thanks. I've seen the BG/L argument, but BG/P processors are faster. I<br> > have no idea how much though, and am looking for actual numbers or if<br> > those are not available a guess based on actual BG/L numbers and some<br>
> argument about scaling to a BG/P.<br> ><br> > Cheers,<br> > Peter<br> ><br> > Mark Abraham wrote:<br> > > Peter Tieleman wrote:<br> > >> Hi,<br> > >><br> > >> Has anyone run benchmarks on a BlueGene/P ?<br>
> ><br> > > The word from IBM in December was that since GROMACS 3.x would lack<br> > > both assembly inner-loops and threading on BlueGene/L, that it wasn't<br> > > worthwhile running GROMACS on onw. I figure that goes for BlueGene/P too.<br>
> ><br> > > Mark<br> > > _______________________________________________<br> > > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> > > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> > Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before<br> > > posting!<br> > > Please don't post (un)subscribe requests to the list. Use the www<br>
> > interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br> > > Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>
> ><br> > ><br> ><br> > _______________________________________________<br> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br> > Please don't post (un)subscribe requests to the list. Use the<br> > www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br> <br> _________________________________________________________________<br> Express yourself instantly with MSN Messenger! Download today it's FREE!<br>
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<br> Message: 2<br> Date: Tue, 01 Apr 2008 09:10:09 +0100<br> From: Hannes Loeffler <<a href="mailto:h.loeffler@dl.ac.uk">h.loeffler@dl.ac.uk</a>><br> Subject: Re: [gmx-users] Blue Gene/P<br> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:1207037409.5122.14.camel@zgb83773vig.dl.ac.uk">1207037409.5122.14.camel@zgb83773vig.dl.ac.uk</a>><br> Content-Type: text/plain<br> <br> Ok, here just a few numbers.<br> <br> System: 52.000 atoms, coarse-grained, 500.000 steps<br>
<br> BlueGene/P: 16(procs) x 4(threads) = 64 tasks (or whatever they are<br> called)<br> 8x4 7.25 h<br> 16x4 11 h<br> 32x4 > 12 h (queue only allows <= 12 h)<br> <br> BlueGene/L:<br> 16x2 10 h<br> 64x2 > 12 h<br>
<br> Note: the procs x threads figures above are the numbers I asked for. It<br> may be possible that the scheduler distributes in a different manner. I<br> don't now.<br> <br> That's all I have for the moment.<br>
<br> <br> On Mon, 2008-03-31 at 17:29 -0700, Peter Tieleman wrote:<br> > Thanks. I've seen the BG/L argument, but BG/P processors are faster. I<br> > have no idea how much though, and am looking for actual numbers or if<br>
> those are not available a guess based on actual BG/L numbers and some<br> > argument about scaling to a BG/P.<br> ><br> > Cheers,<br> > Peter<br> ><br> > Mark Abraham wrote:<br> > > Peter Tieleman wrote:<br>
> >> Hi,<br> > >><br> > >> Has anyone run benchmarks on a BlueGene/P ?<br> > ><br> > > The word from IBM in December was that since GROMACS 3.x would lack<br> > > both assembly inner-loops and threading on BlueGene/L, that it wasn't<br>
> > worthwhile running GROMACS on onw. I figure that goes for BlueGene/P too.<br> > ><br> > > Mark<br> > > _______________________________________________<br> > > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br> > > Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before<br>
> > posting!<br> > > Please don't post (un)subscribe requests to the list. Use the www<br> > > interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> > Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br> > ><br> > ><br> ><br> > _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br> > Please don't post (un)subscribe requests to the list. Use the<br> > www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
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<br> End of gmx-users Digest, Vol 48, Issue 2<br> ****************************************<br> </blockquote></div><br>