VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 15 2016 - 12:22:00 CDT

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
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http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
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