[gmx-users] normal node again

[Anton Feenstra]

Berk Hess wrote:
> 
>> From: Claudio Saburo Shida <shida at biof.ufrj.br>
>>
>> can I use nm (normal modes) analysis to study membrane undulations?
> 
> No.
> Normal mode analysis is a 0 K, at this temperature the structure
> of a bilayer is very different from the one at 300 K.

You should be able to find them from essential dynamics analysis of
an MD simulation (at the proper temperatures).

In the case of a membrane, it could even be that getting this MD simulation
will be less time consuming than the rigorous minimization needed to do the
NM analysis...


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
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|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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