Re: temperature calculations from velocities in NAMD?

From: Sebastian Stolzenberg (
Date: Tue Nov 10 2009 - 23:00:44 CST

Dear Axel,

This is the section that puzzled me:

NAMD User's Guide, Version 2.7b1
5.3.1 Bond constraint parameters

Description: When water is selected, the hydrogen-oxygen and
hydrogen-hydrogen distances in waters are constrained to the nominal
length or angle given in the parameter file, making the molecules
completely rigid. When rigidBonds is all, waters are made rigid
as described above and the bond between each hydrogen and the (one) atom
to which it is bonded is similarly constrained. For the default case
none, no lengths are constrained.

What am I missing about "angles" here?
If "rigidBonds" really refers to bonds only, your approach sounds very

Thank You,

Axel Kohlmeyer wrote:
> On Sun, 2009-11-08 at 20:24 -0500, Sebastian Stolzenberg wrote:
> sebastian,
>> Can I thus assume that "rigidBonds all" really only constrains bonds
>> (for hydrogens attached to non-water heavy atoms)? If no, what angles
>> does NAMD "rigidBonds all" constrain for the protein?
> from which part of rigid_Bonds_ do you infer
> that any angles are constrained as well?
> if you need confirmation, just look at a trajectory.
> you can use VMD to measure the instantaneous values
> of bonds/angles/dihedrals during the trajectory.
> cheers,
> axel.
>> Thank you very much for your help,
>> Best,
>> Sebastian

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