VMD-L Mailing List

From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Fri Apr 15 2016 - 09:19:09 CDT

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