[gmx-users] Waiting for protein-protein MD tutorial...Justin....!!!!

[Justin Lemkul]

On 4/12/14, 5:00 AM, dhaval patel wrote:
> HI Justin We all the users of gromacs are waiting for a
> protein-protein interaction
> MD simulation from you... Please take some time for us and give us an
> awesome tutorial as you have done earlier. Thank you in advance

While I am thrilled that so many people find my tutorials useful, I am unlikely 
to devote any time to writing new ones for the foreseeable future.  There are 
many reasons for this, most prominently the time investment.  It's not simple to 
craft a robust tutorial like the ones I have done, and generally each one takes 
several weeks of time to create, test, refine, and then spend responding to the 
steady stream of people's questions.  I only design tutorials based on work that 
I need to do; I share that information as part of my own learning experience. 
Carrying out simulations solely for the purpose of tutorial writing takes up 
time that I need to spend doing my own actual research and resources that my 
group needs for other purposes.  People frequently request tutorial topics, and 
I'm afraid this is always the answer, largely due to the fact that most requests 
are just sub-topics of an existing tutorial and does not merit its own 
large-scale tutorial.

To this point, there is zero practical difference in setting up and running a 
protein-in-water system and a protein-complex-in-water system.  pdb2gmx does all 
the work for you in reading however many chains you have and writing the topology.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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