[MMTK] Nose-Hoover chain thermostat

Konrad Hinsen hinsen at cnrs-orleans.fr
Tue Mar 20 13:38:53 UTC 2007

On Mar 15, 2007, at 17:22, Yoonjung Huh wrote:

> I can build and install MMTK with such modifications, but the  
> trajectories look different for two thermostats.  I am checking  
> again if I have done this "copying" of NoseThermostat correctly.
> I am wondering though, if there are better ways to implement chain  
> thermostat in MMTK...

Ultimately you have to add the thermostat code to the integrator,  
which is the main part of the work. The points worth considering are

1) Direct implementation in C (or Pyrex) vs. doing a reference  
implementation in Python first. A Python version should not be  
prohibitively slow, and it could make testing the C/Pyrex version  

2) Adding a new thermostat to MMTK's VelocityVerletIntegrator vs.  
writing a simpler integrator (without the pretty messy constraint  
handling, for example) from scratch. In the latter case, you'd have  
simpler code and thus fewer opportunities for mistakes.

3) If you choose to write a new integrator, you might well prefer  
Pyrex to C - I certainly would use Pyrex if I wrote MMTK again today.

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr

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