VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 19 2007 - 18:03:34 CDT

Hi,
  I would expect this to work correctly, but it's possible that
you have an error in your analysis script, or that the CHARMM
trajectory doesn't actually contain PBC cell information for
some reason. Please post the test case you're looking at into the
VMD Public project BioFS area and I'll look at it closely (see
instructions on joining the VMD project below):
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd2ks.uiuc.edu

On Tue, Jun 19, 2007 at 03:59:53PM -0700, Jennie Thomas wrote:
> Hello,
>
> I'm loading a CHARMM coordinate file and then a CHARMM trajectory
> into vmd from an NPT simulation. However, vmd isn't reading the box
> dimensions from the trajectory (even though we've checked to make
> sure they are there).
>
> I'm using the following version of vmd:
> 1.8.6 MacOS X OpenGL Intel 86 (Apple MacOS-X (10.4.7 or later) with
> hardware OpenGL (native bundle))
>
> Any ideas on why the box information isn't available at each step?
> If needed I can post a sample trajectory, coordinate file, and tcl
> script that reads the trajectory and prints out the x box dimension
> at each step (right now this is the same at each step, but it should
> be fluctuating).
>
> With thanks,
> Jennie Thomas 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078