Re: temperature calculations from velocities in NAMD?

From: Axel Kohlmeyer (
Date: Sun Nov 08 2009 - 19:33:18 CST

On Sun, 2009-11-08 at 20:24 -0500, Sebastian Stolzenberg wrote:


> 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.

> Thank you very much for your help,
> Best,
> Sebastian

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

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