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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