[gmx-users] Membrane protein tutorial

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Apr 8 14:13:20 CEST 2009

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



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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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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