VMD-L Mailing List

From: Peter Jones (Peter.Jones-2_at_uts.edu.au)
Date: Thu Jul 20 2006 - 00:43:24 CDT

Hello,

I have an NAMD dcd trajectory in which one monomer of a dimer gets
wrapped to the other side of the cell due to COM motion during the simulation.
I would like to write a VMD tcl script that produces the unwrapped trajectory
so I can measure various intermonomer distances etc.

The simulation used a flexible cell and I think the unit cell info is in the trajectory
file, but I'm not sure how to extract it and use it in this way. Can anybody help?

thanks in advance,

Peter Jones