[gmx-users] Multiple Simulations

[Anton Feenstra]

David van der Spoel wrote:
> Doesn't that depend on the kind of properties? If the simulations are 
> under the same conditions (T,P etc.) then I'd say one can just 
> linearly average most properties.

That depends on the starting conditions, doesn't it? If I would simulate
a protein starting 10 times from an x-ray structure and 10 times from a
rough homology model (or, worse, a high-T unfolded structure), I wouldn't
trust the linear averages...

In other words, the x-ray structures are probably of a lower (free) energy,
making therefore the whole trajectory more 'likely', than those started
from the high (free) energy state. It could come down to assigning (free)
energies to the independent trajectories, which may be as simple as taking
the average potential energy over the trajectory. But I'd like to know if
anyone has done some kind of (rigorous) comparison on methods to do this?


-- 
Groetjes,

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