XAvier Periole wrote:
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote:
Marc Baaden wrote:
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.
In general models that have been parameterized for one specific
observable may not reproduce other observables *unless* the
observables used for parameterization have a clear physical basis
*and* the energy function captures the correct physics. Most
biomolecular force fields (including Martini as far as I know) have
been parameterized to reproduce density and energy of condensed phase
(liquids), and hence this kind of data is usually reproduced quite
well. However mixtures of components (e.g. two liquids) are usually
not reproduced as well.
By doing the kind of pulling simulations, preferably both atomistic
and with CG models, one can try to verify whether the CG models can
actually reproduce force curves to a comparable accuracy as all atom
models. This kind of work should be done *systematically* before any
applications.
What does this boil down to? If you want to apply MD tools to get an
accurate force curve *now*, use all atom models. If you want to play
with and test CG models, then do a large systematic test (many
systems). If the CG models perform reasonably, you have cleared
everyone's conscience and will get a lot of citations. If they don't
then you should try to understand why not. Are there fundamental flaws
in the model? If so, can they be fixed?
This is of course the idea, but then comes the problem of believing that
atomistic simulations
are actually giving the right answer!
Of course, on the other hand CG models were developed to a large extent
by comparison with A models, so if these are wrong, CG models are
hopeless...
In addition, especially for this kind of applications, does the
experimental data measure the same thing that we try to calculate?
Questions, questions.
Have fun.
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.peri...@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.
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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