From: Axel Kohlmeyer (
Date: Wed Nov 09 2005 - 02:12:36 CST

On Tue, 8 Nov 2005, Craig Maloney wrote:

CM> Hi all.

hi craig,

CM> I have a single monolithic pdb file which has what is essentially an
CM> entire MD trajectory in a single file. There are CONECT records
CM> which I understand are not honored by VMD.


CM> file, or will it require some manual intervention? Bonds DO break
CM> dynamically, mind you. I don't know if this is an abuse on my part

that is the critical problem. vmd assumes, that the 'structure' i.e.
the bonding information, does not change during a trajectory. there are
currently two ways to deal with that situation. first you can try
using the 'dynamics bonds' representation, in the hope that it will
reproduce the bonding information like you want to have it. this depends
very much on what kind of atoms you have in your system and how critical
the exact reproduction of the bonding information is. for a simple
example to use that, see, e.g.:

the second option is to create a psf file for _each_ configuration
and load it as a separate molecule and then use some vmd script magic
to visualize it, see, e.g.:

note, if the number or order of atoms changes in your pdb trajectory,
you have to use the second method.

CM> of the pdb spec or not. If some manual futzing would be required, I
CM> would much prefer to do my futzing with x-plor in python as I'm a tcl
CM> novice.

depending on what you really want to see and what kind of data you
have, there may be another option, so please provide some more details
about your files and the system.


CM> It's very convenient for me to have my trajectory sit in a single pdb
CM> file, and VMD understands what I want it to do beautifully now, but
CM> will the approach of a single monolithic pdb file (along with a
CM> corresponding single monolithic psf file) still work when I add bonds?
CM> Anyway, any thoughts would be appreciated.
CM> Thanks,
CM> Craig

Axel Kohlmeyer  e-mail:, web:
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.