From: Axel Kohlmeyer (
Date: Tue Dec 14 2010 - 04:13:41 CST

On Tue, Dec 14, 2010 at 4:26 AM, <> wrote:
> Hi,
> I try to measure the the constants of the bond lengths. The command is the
> following: measure energy bond {5 6} k or measure bond {5 6} k?
> I read the user guide but I am confused.
> If anyone knows, I would be thankful if he could tell me about these commands.
> On top of that, in order to find the multiplicity of a dihedral do I have to pay
> attention to the order of the atoms eg. the chiral center must be first?


this kind of information is usually contained in the force field
parameter file and thus not known to VMD.

there is a parametrization tutorial on the TCBG homepage somewhere
that also explains the (charmm) parameter file format as needed (in
case it is not already self-explanatory to you).

what VMD measures is the "current" value not the parameter (constant?) value.


> Thank you in advance.
> Maria

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.