Re: ABF thermostats and energy introduced into the system

From: Ajasja Ljubetič (
Date: Wed Feb 27 2013 - 06:26:39 CST

Dear All,

I have noticed another minor detail related to the thermostats that is
puzzling me:
*Why does there seem to be discrete periodic noise introduced into the
velocity autocorrelation functions as soon as one turns on the thermostat?
(example image here <>).*

NoTempNoABF1 -- No thermostat and no ABF bias applied
NaABF_LD1 -- Langevin thermostat wiht 1/ps coupling without ABF bias
LD1 -- Langevin thermostat wiht 1/ps coupling and ABF bias
LA50 -- Lowe-Andersen thermostat with 50/ps coupling and ABF bias
tCouple -- Not for using just for checking:)

Some more details: I was checking the velocity autocorrelation function (in
the psi/phi colvars space). I wrote the colvars to the trajectory every 2.5
fs (every 25 steps), and then made the autocorrelation of the differences
between consecutive steps.
The velocities are uncorrelated as expected, but all velocity
autocorrelation in the first row that have a thermostat show some discrete
levels. These are really small values, so it's probably just noise, but why
is it discrete?

Thank you and best regards,

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