Re: temperature calculations from velocities in NAMD?

From: Sebastian Stolzenberg (
Date: Sat Nov 07 2009 - 19:49:18 CST

Hi Axel,
> very simple: each "shaken" bond or angle is equivalent to
> removing one DOF. so waters have 6 DOFs instead of 9. if
> you go to more complex constraints it can become very complicated.
SHAKE *angles*?? The NAMD tutorial doesn't mention anything about them.
Or was your reasoning now more in general for educational purposes?

Would you have some DOF reading recommendations at hand for the more
complicated (e.g. dihedral) constraints cases? (just for my own
curiosity and to maintain my astonishment :o) )

Thanks a lot,

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