VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Apr 15 2016 - 09:50:05 CDT

Dear Laura,

Thank you for your report. Can you send me your input files off-list?

Best,
Jerome

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
>