Quoting Radhika Jaswal <[EMAIL PROTECTED]>: > 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, [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 > > **************************************** > > > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
