[gmx-users] Denaturation of Proteins by MARTINI Coarse-Graining Forse Field

XAvier Periole x.periole at rug.nl
Wed Dec 16 12:26:45 CET 2009

Is this a real gromacs-user question?

Have your tried to contact the MArtini developers?

As a matter of fact some of them have prepared a new MARTINI
web-site where a discussion forum will be on.

To answer your question: using MARTINI for the unfolding
mechanism of proteins would be very challenging to put it nice.
It is not "AT ALL" made for that!

The use of Go-model has be tested (for other purposes) and
it would be at least as "bad" as using an all atom FF. No need
to use a CG model with Go-models, atomistic are fast enough.
Well that is my current opinion.

On Dec 16, 2009, at 11:36 AM, rasoul nasiri wrote:

> Dear GMX users,
> Hi
> I'm working on denaturation of proteins with MARTINI CGFF by Gromacs  
> suit.
> according to this paper (J. Chem. Theory and Comput. 2008, 4, 819– 
> 834) I undestand there is a limitation for modeling of folding and  
> unfolding with MARITI CGFF for systems in which the folding and  
> unfolding of secondary structures are playing a substantial role are  
> therefore not suitable for modeling with current CG force field.
> since I perform CGMD simulation on tertiary structure, is there this  
> limitation on my system or no?
> If your question is positive, Is there an improved version of  
> MARTINI CGFF for doing it?
> Can I use Gō model for resolve of this problem?
> What is your idea about this problem?
> I'm looking forward to hearing from you about this matter!
> Beast Regards
> Rasoul
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