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. [email protected] 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:[email protected] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
