[gmx-users] Re: implicit solvent and REMD

[Anton Feenstra]

Xavier Periole wrote:

> Wei Fu wrote:
> 
>> Hi, I want to observe the unfolded state of a protein with 370 residues,
>>
> unfolded stateSSSSSSS !!! For sure a 370 residues protein must have a lot of
> unfolded states. I think that this information is unaccessible at the time except
> if you have thousands of processors available for a long time.

For given unfolding conditions (e.g., high T, high P, high Urea), there
is *one* unfolded state. (By definition!)

However, what I think Xavier wanted to say is this state will consist of
many conformations. And he is right again in pointing out that for a protein
one cannot hope to learn much in a reliable way about the unfolded state
conformations from an MD simulation. You can certainly unfold the protein
fast (try, e.g., T=4000K), but that unfolded state may not be relevant for
what you want to do, or you can try and do it slow, but then you may not
reach the unfolded state in any reasonable amount of time.


-- 
Groetjes,

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