From: Karteek Kumar (
Date: Fri Apr 15 2016 - 09:50:19 CDT


The dihedral value of same four atoms should be equal either you calculate
using colvars or VMD.

How much different the values are?
I am afraid, if you are measuring the dihedral of different atoms.
Can you double check the atoms?

Remember, the colvars atom numbers start with 1.
In VMD, serial starts with 1 and index starts with 0.

Hope it helps !!!


On Fri, Apr 15, 2016 at 7:49 PM, Laura Joana <>

> Dear all,
> I'm having a problem with colvars module. I have a dcd file with just one
> frame. I wrote a script to run in VMD and get two dihedral angles using
> colvars module. So I have a colvars configuration file that defines the
> groups to calculate the dihedrals like I normally need. Everything works
> fine.
> Then I made a config file for NAMD that only reads the same dcd file and
> make "run 0". Then, using the *same* colvars configuration file, I print
> the dihedral angles.
> I supposed I would obtain the same values, as I just ran zero steps
> before, but that is not the case. I'm obtaining different values! Can
> someone explain me why? Or, has someone here already had the same problem.
> My system is just the di-alanine molecule in vacuum.
> Thanks,
> Laura