VMD-L Mailing List

From: Bob Johnson (robertjo_at_physics.upenn.edu)
Date: Thu Aug 18 2005 - 12:00:19 CDT

Hello everyone,
Right now I am simulating the interaction between single stranded DNA and an
infinite nanotube in GROMACS. In a typical trajectory, the DNA adsorbs to the
tube and slides along the outer wall of the tube. Sometimes the DNA slides too
far and a portion of it ends up in the next box. Of course, VMD shifts this
portion of the DNA back in the original box. However, VMD draws bonds between
the original DNA molecule and the shifted piece. Is there anyway to turn this
feature off?

GROMACS has a program called trjconv that applies formatting to trajectories. It
has a bunch of options for how the periodic boundary conditions are handled.
I've tried everything this program has to offer with no success. It seems that
it's a problem with VMD.
Thanks,
Bob Johnson