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, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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 <[EMAIL PROTECTED]> > Subject: RE: [gmx-users] Blue Gene/P > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > 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: [EMAIL PROTECTED] > > To: [email protected] > > 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 > > > _______________________________________________ > > > gmx-users mailing list [email protected] > > > 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 [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080401/8d0d044f/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Tue, 01 Apr 2008 09:10:09 +0100 > From: Hannes Loeffler <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Blue Gene/P > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > 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 [email protected] > > > 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 [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 48, Issue 2 > **************************************** >
_______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
