Vmd Simulation

LAMMPS Users,

I am utilizing bead-spring models of polymeric molecules in my graduate research and I want to use one of the openly available graphics software packages to render my molecular models. I wish to specify the molecular topology so that whichever graphics package I use will only draw the bonds that I want it to draw; furthermore, I want to generate movies of my simulations so I would like a package that permits automation of image generation.

I think I can do this with VMD. Indeed, I have prepared “pdb” files of my molecule, including “CONNECT” records, and attempted to use these in VMD. However, the code cannot properly find bonds for my system.

Please provide any advice as to how I achieve my desired results and thanks in advance for your help.

Happy simulating!

This sounds like a VMD question - maybe Axel can point
you in the right direction.

Unless every other graphics package can read PDB
files and CONNECT info, your quest for universal
portability is likely to fail.

Steve

This sounds like a VMD question - maybe Axel can point
you in the right direction.

this is a repeated post and i already
answered the question.
it should be in the mailing list archives by now.

axel.