From: Joe Janicki (
Date: Mon Jun 13 2011 - 13:36:18 CDT


I am trying to analyze .dcd trajectory files.

Is there a way to automate the VolMap Tool to produce a .dx file for every
frame in the trajectory? I'm working with thousands of frames, and it would
be unreasonable to do each frame individually. I'd like two separate files
for each frame- a .dx of the structure being studied and a .dx of the waters
in the system. Is it possible to write a script to automate this? Any
pointers would be appreciated since I'm new to programming in VMD.

I would then like to edit the .dx files using another program. I can save
the output from that program in either .dx or .pdb format (in a single file
made from the two files I previously described).

>From the thousands of .dx or .pdb files I generate from that program, is
there a way to make a single file that I could load into VMD (similar to a
trajectory file) that would have separate frames? Essentially, I'd like to
overlay the original .dcd with the files I edited (a unique .dx or .pdb
added to each frame of my original trajectory). If not, writing a simple
script would solve that, right?

Any ideas on how to do (any) of this would be excellent. I'll update if I
figure out how to do any of this.

Thank you,
Joseph Janicki