Re: temperature calculations from velocities in NAMD?

From: Axel Kohlmeyer (
Date: Sat Nov 07 2009 - 14:21:40 CST

On Sat, 2009-11-07 at 14:32 -0500, Sebastian Stolzenberg wrote:
> Dear All,

dear sebastian,

> Maxwell-Boltzmann tells us that for an ideal gas with particles of mass
> m, e.g.:
> sqrt(<v^2>)=sqrt(3kT/m)
> Could somebody refer me to papers describing, how in NAMD, temperatures
> are calculated from velocities (with systems of particles that interact
> and all have different masses)?

try a text book on MD (or stat mech) instead. the temperature of
a group of particles is usually computed from its kinetic energy
and the available degrees of freedom:

T = Sum_i (m(i)*v(i)^2) / (n_DOF*k_B)

the iffy part is often to determine the exact number of DOFs.
without shake this is usually 3n-3.

> I hope this calculation is not performed by solving the Langevin
> equations for temperature? :o)



> Thanks,
> Sebastian

Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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