Re: temperature calculations from velocities in NAMD?

From: Sebastian Stolzenberg (
Date: Sat Nov 07 2009 - 20:13:55 CST

.. Apologies, just saw the NAMD note on SHAKE *angles* for water.

I assume now that the SHAKE algorithm imposes restraints on all the IC
coordinates involving the particular hydrogen to be constrained.

Then, what if I have a hydrogen attached to a backbone nitrogen? What
about hydrogens attached to carbons along the side chains?
I am worried to have to deal with dihedral constraints to determine
n_DOF..... although the original SHAKE paper by RYCKAERT JCP 1977 does
not mention dihedrals...

Thanks a bunch,

Sebastian Stolzenberg wrote:
> 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,
> Sebastian

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