[gmx-users] Re: gmx-users Digest, Vol 7, Issue 4

Michel Cuendet michel.cuendet at epfl.ch
Tue Nov 2 17:53:56 CET 2004

Hi gromacs fans,

Is there a justification for not using a nose-hoover chain thermostat in 
gromacs, or is it just not yet implemented?

 From what I know, the single nose-hoover thermostat does not in theory 
reproduce a canonical ensemble, if there are other constants of the 
motion for the unperturbed system than just the energy (eg. the 
momentum, or center of mass velocity). See Tuckerman et al, JCP 
115(4):1678,2001. It seems that for big (sufficiently mixing) systems 
however this issue is not too severe.

There is  another undesired effect : the Toda Demon, see Holian et al 
Phys Rev 52(3) : 2338, 1995. If the coupling constant is not set 
properly, the demon hidden in the Nose-Hoover dynamics will generate 
slow modulations of the temperature, whereas the normal temperature 
fluctuations will differ from those related to a canonical ensemble. A 
chain should cure this.

Also, shouldn't the nose-hoover extended variable be integrated together 
with the positions and momenta, with a integration scheme more accurate 
than xi[i] += dt*Qinv*(T - To) ?



Michel Cuendet, Ph.D. student
Laboratory of Computational Biochemistry and Chemistry
Swiss Federal Institute of Technology in Lausanne (EPFL)
CH-1015 Lausanne						
Switzerland                            Phone : +41 21 693 0324
lcbcpc21.epfl.ch/~mitch	                       +41  1 633 4194

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