Subject: Re: CCL:Confusion on ensemble average for biomolecule

From: Konrad Hinsen <[email-masked]>
Date: Thu, 17 May 2001 19:24:36 +0200

> THEORETICALLY, should we do sampling of initial
> velocities for a large number of trajectories to let
> the STATISTICAL MECHANICS make sense? However, in
> reality, it's impratical to do that. 

Usually one assumes that the system is ergodic, i.e. reaches any point
in phase space if one waits long enough. Then a time average over a
single trajectory is equal to an ensemble average over many
trajectories with different initial conditions.

Unfortunately, real MD trajectories for macromolecular systems are
never long enough to assume sufficient sampling of all coordinates.
Usually they are even too short by at least an order of magnitude. One
attempt to overcome this is to run several trajectories from different
initial conditions that are reasonably independent - that means not
only different velocities, but also different initial configurations.
-- 
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