VMD-L Mailing List

From: DreamCatcher (huangshuping1987_at_gmail.com)
Date: Fri Apr 29 2011 - 07:48:18 CDT

Dear vmd-developers,

I am recently using LAMMPS to do some Molecular dynamics simulation. I have
two questions to post here.

First, when I use version 1.9 of vmd to visualize the dump file from the
simulation. Unfortunately, THE BONDING information is a little wierd as the
end-point hydrogens which connect to the same carbon form bonds between each
other. I have looked through the documents related to topotools trying to
figure out a solution, however, failed. Nothing about post-processing a
trajectory files with TCL scripts has been found. Is there any other scripts
I can resort to to accomplish such a post-processing work? Or is there
something I missed?

Second, When I do my MD simulation with reax/c codes, the trajectory outputs
are a little different from those usual dump files due to the extra control
file designated before the MD run. And I have had some bond and angle
informations dump to the trajectory files. When I use vmd to view the
trajectory, I failed. VMD 1.9 cannot recognize the format. What can I do to
resolve such a problem?

       Any reply will be appreciated. Thank you in advance!

Cheers,
-Shuping Huang