[gmx-users] Membrane protein tutorial

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Apr 8 09:32:33 CEST 2009

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 :)



On 4/8/09, Justin A. Lemkul <jalemkul at 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
>  ========================================
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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

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