[gmx-users] Pulling a CG protein

XAvier Periole x.periole at rug.nl
Thu Jul 30 11:56:24 CEST 2009

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!
> 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.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.
> -- 
> 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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