[gmx-users] Membrane protein tutorial

[Justin A. Lemkul]

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 <jalemkul at 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 <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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>>>
>> --
>> ========================================
>>
>> 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

========================================