VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 08 2010 - 09:37:25 CST

Hi,
  Likely the easiest method of producing a trajectory file that you
can load into VMD is to generate an XYZ file, a very simple text
file format that is easy to write and to read:
  http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html
 
I have attached examples for you, to make a trajectory, you merely
need to repeat the structure of the file multiple times as I've done
for the trivial trajectory example (I just concatanated the original
structure multiple times).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 05, 2010 at 04:53:01PM -0500, Wallace Dumars wrote:
> Hello,
> I am a new user to VMD. I am currently reading and working
> through the tutorials entitled "Using VMD", "VMD Images
> and Movies", and "Bionanotechnology Tutorial" in order to
> obtain a better understanding of VMD.
> However, before I proceed, I was wondering if I could gain some
> assistance with a basic question.
> My question involves how to load coordinate data into VMD and
> create movies using this data.
> I have trajectory data (x, y, and z coordinate data as a function of
> time) that I would like to "load" into VMD and make a movie of
> the movement of my structure.
> So, just imagine a particle bead interacting with a surface of beads.
> I have the coordinates of the surface and the coordinates of the particle
> as a function of time, now I want to make a movie of the trajectory.
> (I do not have a .pdb file of either my particle bead nor of my surface. I
> just have coordinates).
> However, I am a little confused about how to do this (of if this can
> be done at all).
> Upon first glance (although I am not too sure how to do this) it appears
> that I would have to write a script, using the graphics commands, to draw
> my "scene" at every instance in time and then use those frames to create
> the movie.
> Am I thinking about this correctly or is there another solution to my
> problem?
> Thanks again for your time and assistance,
> Wallace. 

-- 
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