VMD-L Mailing List

From: Bob Johnson (robertjo_at_physics.upenn.edu)
Date: Mon Aug 08 2005 - 10:42:13 CDT

Hello,
I am doing some simulations in GROMACS with carbon nanotubes. Initially VMD
recognizes the C-C nearest neighbors and draws bonds between them. However,
when I view the trajectory generated by GROMACS VMD no longer draws the bonds.
In addition to a trajectory, GROMACS generates a restart file that contains the
last frame of simulation. When I view this restart file in VMD, the bonds are
drawn. Do es anyone know how to visualize the bonds throughout the whole
trajectory and why VMD doesn't draw them in automatically?
Thanks,
Bob Johnson
University of Pennsylvania