[gmx-users] RE: נושא: RE: Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain

Inon Sharony InonShar at TAU.ac.IL
Mon Jul 16 13:46:02 CEST 2012

I thought setting tau_t=0 for some of the groups means that they're not
coupled. That is tau_t would in fact be infinite, but that would be more
difficult to input, whereas if tau_t were actually equal to zero the
situation (as you described it) would lack physical significance...
Since only the Nose-Hoover thermostat gave me any trouble with setting
tau_t=0, I thought this was already set as described above for all other
thermostats (not including the SD thermal-coupling scheme).
This was addressed in the past by Mark, David, you and myself :


And also:


If my system is [ 0 1 ], my t coupl grps are [ 0 1 ] (i.e. diatomic,
thermal-coupling group for each atom), and I want to tell GMX to thermally
couple atom 1 with tau_t=1ps and NOT couple atom 0 at all:
How would I do so in v-rescale?
How would I do so in Nose-Hoover?
How would I do so in SD?

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