[gmx-users] Pulling a CG protein

[Marc Baaden]

Hi Xavier (and Johnny),

I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least qualitatively
they behave quite reasonably, although these models have never been
parameterized or systematically tested with this kind of application in
mind.

What I mean by qualitatively is that I wouldn't trust a force-extension
curve of such simulations (unless you do some force-matching :)) - re:
FD144), but the conformational changes that are observed in a moderate
pulling regime do seem to make sense.

The experiments we carried out were interactive pulling experiments,
either to induce opening and closure of the guanylate kinase enzyme or
to explore the membrane anchoring and the mechanical properties of the
SNARE complex. This is briefly described in reference [1].

Cheers,
Marc


[1] http://dx.doi.org/10.1002/jcc.21235
    O. Delalande, N. Férey, G. Grasseau and M. Baaden:
    Complex Molecular Assemblies at hand via Interactive Simulations,
    2009, J. Comp. Chem.


x.periole at rug.nl said:
>> Hi Johnny,
>> I am not familiar with pulling and even less with gromacs but I would
>> be very cautious in using the MARTINI force field for the kind of
>> simulation you are doing. This CG model has not been tested at all
>> for this and it might not be very good at it! But I would be very
>> interested in knowing how it   actually perform.

>> XAvier.




-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217