Tsjerk Wassenaar wrote:
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).
Indeed, a single page is quite simple, here you go:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/tutorial.html
I'll fix up the lysozyme tutorial and add some discussion on PBC. Thanks for
the tips!
-Justin
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
========================================
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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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--
========================================
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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