[gmx-users] Pulling a CG protein
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jul 30 12:10:04 CEST 2009
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
>> 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
>> 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
In addition, especially for this kind of applications, does the
experimental data measure the same thing that we try to calculate?
>> 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 .
>>>  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.
>> 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.
>> spoel at xray.bmc.uu.se spoel at 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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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