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 <[email protected]> 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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--
========================================
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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