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

[Justin A. Lemkul]

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:

http://www.gromacs.org/Documentation/How-tos/Parametrization

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.

-Justin

> 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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