[gmx-users] Pulling a CG protein

Marc Baaden baaden at smplinux.de
Thu Jul 30 12:34:59 CEST 2009


Just picking up the following bits of the conversation:

David van der Spoel wrote:
>> What does this boil down to? If you want to apply MD tools to get
>> an accurate force curve *now*, use all atom models. [..]

x.periole at rug.nl said:
>> This is of course the idea, but then comes the problem of believing  
>> that atomistic simulations are actually giving the right answer!

I think this is actually quite a valid point. As David pointed out, 
many forcefields have been parameterized with respect to density and 
energy data. So there is actually no guarantee that atomistic 
forcefields do particularly well with respect to pulling simulations
(although many people have used them for such simulations). 
The gold standard should probably be to compare CG pull simulations 
directly to corresponding experimental data whenever possible.

So have even more fun :)

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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