VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Dec 01 2011 - 22:28:12 CST

On Dec 1, 2011, at 10:45 PM, Joey Vella <jovella62890_at_gmail.com> wrote:

Hi Joseph,

> Hello,
> My name is Joseph Vella and I'm an undergraduate at Rutgers University. Currently I have a text file of 200000 configurations of a system containing 128 diatomic molecules from a Monte Carlo Simulation. The text file contains the X and Y coordinates of each molecule along with the orination of each molecule for all configurations. I was wondering if it would be possible to view a configuration or a "movie" of the configurations from the text files using VMD?

Short answer: No and Yes.

Long answer:
The "no" stands for: not without some programming done by you. In
order for VMD to be able to read a file, it has to know about its
format. That is typically done in a plugin (molfile plugin library)
written in C (or C++), but it can (with a performance penalty) also be
written in Tcl script (topotools plugin). Also you'll have to convert
the data into individual atom positions (and bonds).

The "yes" stands for: it has been done before. E.g. the LAMMPS plugin
does this kind of conversion for dipole data, if a certain enviroent
variable is set. Another option would be to write a standalone program
or script that will convert your data file to a format that VMD
supports.

Cheers,
      Axel.

>
> Thank you.