Hi Justin, Pretty neat. Thnx! Just a few comments, also on the lysozyme one. I think it's best to name and explain all options you use for a program, to take as much of the 'magic' out as possible. Having unexplained options may make students, mainly undergrads, go into a non-absorbant mode, just entering commands the cook-book style. Of course, that's not an issue for people wanting to get to understand these things, but then an extra line of explanation also never hurts. For the lysozyme thing I also noted you used a cubic box. I think it's best to use a rhombic dodecahedron and just pretend that that's the common way of doing things when simulating proteins in solution.
But the real reason for replying is to ask whether you have this available in a single pretty-print formatted page? I would like I handout of this :) Cheers, Tsjerk On 4/8/09, Justin A. Lemkul <jalem...@vt.edu> wrote: > > Hello all, > > Due to the recent influx in questions related to membrane proteins > (especially with common questions), I decided to put together a step-by-step > tutorial for membrane protein systems. It's a work in progress, so I would > genuinely appreciate feedback from anyone who has a few minutes to take a > look. These procedures make sense in my head, so hopefully that comes > through in the instructions :) > > I have posted a link on the wiki site to my tutorial: > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html > > I hope that people find this useful. I have attempted to walk the user > through most practical concerns that arise regarding topology organization > and a few analysis questions that show up on the list frequently (g_order, > g_density, etc). > > If you have comments or questions, please do not hesitate to send me a > private message. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php