On Fri, Sep 23, 2011, Brian Radak wrote:
>
> Does this difference in degrees of freedom have any bearing on the dynamics
> or is it just a quirk of the output?
I would have thought that the thermostat would have been affected, and hence
the velocities on two sides. But if that happened, the kinetic energies would
not be equal, and very quickly the coordinates and potential energies would
not match. Since that is not happening, it looks like just a quirk in the
output.
I must say that having an O-H bond cross the QM/MM boundary sounds very odd.
We certainly never looked at anything like this when developing or testing the
code. Let's see how Qiantao's fix works out.
...dac
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Received on Sat Sep 24 2011 - 06:00:04 PDT
