VMD-L Mailing List

From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Sat Apr 16 2016 - 05:16:22 CDT

Thanks Jerome! If that solves my problem I'll always going to include that
command line in my script when no periodic box information is given.
Best,
Laura

2016-04-15 19:22 GMT+02:00 John Stone <johns_at_ks.uiuc.edu>:

> Hi,
> A very minor correction. Current VMD versions do set the periodic cell
> sizes to zero by default. That being said, there likely may still exist a
> molfile plugin or two that may be setting the periodic cell size to
> a non-zero number by default.
> Another possibility is that you may have loaded a file that had been
> processed
> by an old version of VMD that indeed did exactly what Jerome is warning
> about.
>
> Cheers,
> John
>
> On Fri, Apr 15, 2016 at 06:50:32PM +0200, Jérôme Hénin wrote:
> > Hi Laura,
> > The problem comes from a very unfortunate default behavior of VMD:
> when no
> > periodic box information is provided in a DCD file, it sets the box
> sizes
> > to 1, which breaks PBC-aware codes like colvars.
> > You can set them to zero with
> > molinfo top set {a b c} {0 0 0}
> > then the dihedral values are correct.
> > Best,
> > Jerome
> > On 15 April 2016 at 16:50, Karteek Kumar <[1]karthik3327_at_gmail.com>
> wrote:
> >
> > Hi,
> > 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, A if you are measuring the dihedral of different
> atoms.A
> > Can you double check the atoms?A
> > Remember, the colvarsA atom numbers start with 1.
> > In VMD, A serial starts with 1 and index starts with 0.
> > Hope it helps !!!
> > Thanks
> > Karteek
> > On Fri, Apr 15, 2016 at 7:49 PM, Laura Joana
> > <[2]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
> >
> > References
> >
> > Visible links
> > 1. mailto:karthik3327_at_gmail.com
> > 2. mailto:laurajoanalopes_at_gmail.com
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>