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!
Chandresh Thakur
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.
VMD can do this. check this out:
http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks#TOC-Reconstruct-a-.pdb-.psf-files-from-
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.
the corresponding pdb record is called CONECT
axel.