Re: temperature calculations from velocities in NAMD?

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Sat Nov 07 2009 - 16:31:48 CST

Thank You, Axel,
> 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.
>
1.)
Sweet, so please let me understand the logic of "n_DOF=3n-3":
for the DOFs, we have
3 for overall translations
3 for overall rotations
and 3n-6 for the fundamental oscillations

Since we only consider kinetic energies for the temperature, we do not
count the fundamental oscillations twice.
Then, n_DOF=3n-3 because we can ignore the 3 translation DOFs (change of
reference frame).
Why not also ignoring the 3 overall rotations to get 3n-6? Maybe it
doesn't matter because
3n-3 ~ 3n ~ 3n-6, since 3n is large....

2.)
Too bad though I am using shake. Fixed bonds reduce the DOFs, so how
does NAMD calculate n_DOF then?
By the way, is there a nice TCL script/NAMD trick calculating T from the
velocities, or would I need to dig into the source code to see how this
is done and write some code myself?

Thank you very much,
Sebastian

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