On Jul 30, 2009, at 12:10 PM, David van der Spoel wrote:
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,
Yes on data from A models that were compared to Exp data, so as much
reliable as possible :))
so if these are wrong, CG models are hopeless...
Well now we use CG to (re)parameterize AT models ... just kidding ...
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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