TopoTools tutorial won't work

Hi everyone,

I’m following Axel’s online TopoTools tutorial, but topotools won’t generate bonds without the simplexyztodata.tcl file, download instructions of which aren’t included. What can I do?

All the files mentioned on Homepage of Axel Kohlmeyer - Tutorial - Part 1
are attached to the same page in a list at the bottom. This is how Google Sites handles this.

Besides, if you combine the various commands the page is commenting on into a file, you would get effectively the same file.

Yes sir, I saw the files. I downloaded and successfully loaded it to VMD, but I have no clue how to implement simplexyztodata.pcl since i’m using VMD on a HPC via SSH. This is the path to the VMD executable. Where do I download the file so it can be read and implemented by the vmd console?

Two things:

  • This discussion is now becoming seriously off-topic. This has nothing to do with LAMMPS anymore, but is about VMD. Thus please direct any further questions about VMD to the VMD-l mailing list.
  • What you are doing makes no sense and that is an indication that you have not properly learned how to use VMD scripting from the VMD manual. The various tutorial files have no place in your VMD installation.

Same as with simulations, you create a working directory for your (tutorial project) and place your various files (coordinate and scripts) there. This is also where you want the created files to appear.
Then you execute VMD from the command line to run the script (no console, no GUI needed). The tutorial is showing that. I quote:

The last script command quit terminates the VMD session, since this script is meant to be run in batch mode via:

vmd -dispdev text -e simplexyztodata.tcl

If you insist on running the script from the console you can launch VMD with vmd -dispdev text and then execute play simplexyztodata.tcl, but then you need to comment out the trailing quit command as explained.