VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 20 2007 - 10:55:34 CDT

Hi,
  The problem is that your box-dim.tcl script is not advancing
the active frame correctly, because you were missing a 'molinfo'
at the beginning of the line:
  set frame $i
Correcting that to:
  molinfo top set frame $i

...cures the problem.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 19, 2007 at 04:28:12PM -0700, Jennie Thomas wrote:
> Hi John,
>
> Thanks for your fast response. I have uploaded one case to the
> following folder:
>
> box-test
>
> under the VMD Public filesystem. I also uploaded a short .tcl script
> that should just read the trajectory and then print out the box
> dimension for each step. I've uploaded both the pdb and CHARMM
> coordinate files, but it doesn't matter which I use. These
> simulations were run by the MacKerell group, I asked them to check
> these are really constant pressure. They confirmed that the box
> information is there and also confirmed these are really constant
> pressure.
>
> Thanks for your help with this.
> Jennie
>
> On Jun 19, 2007, at 4:03 PM, John Stone wrote:
>
> >
> >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 

-- 
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