[gmx-users] Membrane protein tutorial

[Justin A. Lemkul]

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

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