Hi Justin, A handout may be as simple as an all-in-one html page :) I think that especially for teaching you want to use a rhombic dodecahedron to 1. teach good habits and 2. explain PBC (jumping molecules).
Cheers, Tsjerk On Wed, Apr 8, 2009 at 12:59 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > Hi Tsjerk, > > Thanks for the comments. I'll think about adding some tips and tricks > related to other box types; it may be useful when new users ask, "why does > my system look so funny?" The lysozyme tutorial was intended to be a > teaching tool for us, anyway, as we are developing a new course within our > department related to molecular modeling. > > As for a handout of the tutorial, I do not have one at the moment, but I'd > be happy to send one to you when I do. I have my prelim/qualifying exam > next week, so I'll be a bit tied up until then! > > -Justin > > Tsjerk Wassenaar wrote: >> >> 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-us...@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 >>> >> >> > > -- > ======================================== > > 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-us...@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