[gmx-users] Tips and tricks to make your own coarse-grained model?

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 9 14:44:40 CEST 2009

ms wrote:
> Justin A. Lemkul ha scritto:
>>> My aim is to re-implement a formerly standalone CG model by mean of gmx.
>>> It seems that gmx is well suited to the task; however I understand that
>>> there is an incredible number of pitfalls where a newbie fall in.
>>> I am currently reading and re-reading the manual, looking at the online
>>> docs and tutorials. But most of information, understandably, refer to
>>> all-atom modeling and there is little on how to build your own model
>>> on gmx.
>>> Maybe my googling skills are not as good as once they were -in this case
>>> can anyone point me to any page where this kind of task is documented?
>>> If such a page there isn't (and even if there is), I would appreciate a
>>> lot if anyone of you can share your wisdom on best practices, pitfalls,
>>> things to know etc. before diving head-on in such an endeavour.
>> So, to clarify, this is an already-existing CG model that you simply
>> want to use for simulations in Gromacs?  It is then rather easy.  You
>> need to define all appropriate force field files (nb.itp, bon.itp, .atp,
>> etc), and perhaps .rtp files if you can also come up with a way to
>> define an appropriate CG input for pdb2gmx.
> Yes. I know the specs of the cg model, and I want to re-implement it
> within gromacs. Actually it is a class of related models. I'd start from
> a very minimal one and then improve gradually.
> I understand I have to define all appropriate FF files, but I wonder
> what is the best way to do it, what documentation to learn by heart,
> what sanity checks... You make me optimist in saying "it is rather easy"
> , but science is always full of traps, especially for the newcomer...

If the model has been created, tested, and validated, the hardest work is done. 
  You just have to type in a text editor to put it all together :)  If you are 
looking to derive new parameters, well, then that certainly is quite difficult:


Chapter 5 in the manual contains all the information necessary (in terms of both 
syntax and content) for producing the necessary files.  It should be the first 
port of call when questions arise.


> thanks!
> m.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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