VMD-L Mailing List

From: Philippe Bopp (philippebopp_at_REMOVE_yahoo.com)
Date: Fri Apr 15 2016 - 11:29:02 CDT

 do you get something like 180-alpha, or 360-alpha instead of alpha?

 Philippe

On 15 April 2016 at 16:19, Laura Joana <laurajoanalopes_at_gmail.com> wrote:

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