VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 06 2004 - 18:25:44 CST

Mauricio,
  I don't recall what version of VMD you're using, but if its anything
older than VMD 1.8.2, you wouldn't have the most recent version of the
DCD reader plugin (I assume that's the trajectory format you're using
with Charmm right?). Assuming you've got VMD 1.8.2 and are using the
DCD trajectory format, it might be that you don't have Charmm configured
to save periodic cell records in the trajectory. Double check that
you've told Charmm to record the periodic cell info with each timestep
and let us know if you're still unable to read it into VMD 1.8.2.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 06, 2004 at 02:32:31PM -0500, Mauricio C. Tripp wrote:
> Cool! I wasn't aware of the 'periodic' tab, sorry.
> Now, I'm reading a charmm dcd trajectory file for
> an NPT simulation. I guess VMD doesn't read the
> correct box size for each frame; when I click
> on the +/- x-,y-,z-button the corresponding image cell
> is displayed but almost on top of the central cell.
> However, if I run the script set_unitcell.tcl it
> places the image cell acording to the box
> dimensions I use as parameters for the script.
> My next problem is that since I'm looking at a
> NPT simulation, the box dimension will change from
> frame to frame. Is there a way to modify the script
> so it would set the correct box dimensions to
> each frame and just not the same parameters for
> the whole trajectory?
>
>
>
>
> >===== Original Message From axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de =====
> >On Tue, 6 Jan 2004 11:25:51 -0500 "Mauricio C. Tripp" wrote:
> >
> >> Hi all,
> >>
> >> does anyone know an easy way to display the
> >> periodic image cells once I load the central
> >> box into VMD, not just wrap the atoms in it?
> >> any script to do this for a trajectory?
> >
> >hi mauricio,
> >
> >you won't need this with a sufficiently current
> >vmd version. there is a tab 'periodic' in the
> >graphical representation menu. just click on
> >+/- x-,y-,z-button and you'll get copies of your
> >unit cell for the current representation.
> >in case your coordinate file(s) do not provide
> >sufficient information about the unit cell,
> >or vmd does not (yet) read this information,
> >you need to run a small script like the attached tcl subroutine
> >to set the unit cell parameters for each frame of your
> >trajectory.
> >
> >hope this helps,
> > axel kohlmeyer.
> >
> >>
> >>
> >> thank you
> >>
> >> Mauricio C. Tripp
> >>
> >
> >--
> >
> >=======================================================================
> >Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> >Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> >Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> >D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de
> >=======================================================================
> >If you make something idiot-proof, the universe creates a better idiot. 

-- 
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