VMD-L Mailing List

From: Jennie Thomas (jenniet_at_uci.edu)
Date: Mon Nov 20 2006 - 22:09:12 CST

Hi VMD experts,

I have an analysis code (separate from VMD) that reads in AMBER
coordinate files. Someone has asked if I can use this code to
analyze a dcd trajectory, so I decided to try and use vmd to convert
from dcd to crdbox format. However, the box information is not
preserved when doing this. Because this is a constant pressure
simulation I need to use the box information at every step. Do you
know how to force vmd to write box information?

I have a simple tcl script I am using:

# Load the system and the trajectory
mol new "box.cor" type cor

mol addfile "00.trj" type dcd waitfor all
mol addfile "01.trj" type dcd waitfor all

animate write crdbox traj.crd

Do I need to be doing something more complicated to get box
information? Or does anyone have another suggestion for a file
format conversion tool?

Thanks,
Jennie Thomas