Scientific visualization and analysis software for atomistic simulation data and molecular dynamics: ovito (and VMD)

There are a lot of software for this purpose. I select here only two softs.

OVITO

OVITO : http://www.ovito.org/
is a scientific visualization and analysis software for atomistic simulation data developed by Alexander Stukowski at Darmstadt University of Technology, Germany. The program is Open Source and freely available for all major platforms.
Molecular dynamics (MD), molecular statics and Monte-Carlo based simulations are nowadays standard methods for modeling materials with atomic-scale resolution. Such atomistic simulation models generate three-dimensional atomic configurations or trajectories, which usually need to be further analyzed in order to generate new scientific insights. Powerful analysis and visualization techniques play a key role in this process as simulated systems become larger and more complex. Without the right software tools, key information would remain undiscovered, inaccessible and unused. The task of visualization packages such as OVITO is to translate the raw atomic coordinates into a meaningful graphical representation and enable an interpretation by the scientist.

It looks like the current version of OVITO only supports atom_style
atomic.  
Here are a list of alternative programs which can generate bonds,
angles, dihedrals, and impropers:

http://lammps.sandia.gov/threads/msg45535.html
http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1
http://montecarlo.sourceforge.net/emc/Welcome.html   (EMC)
http://sourceforge.net/projects/moleculardynami/
http://lammps.sandia.gov/prepost.html

VMD

The simple VMD: http://www.ks.uiuc.edu/Research/vmd/
VMD is designed for modeling, visualization, and analysis of systems (such as proteins, nucleic acids, lipid bilayer assemblies, etc.)  It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

• Support for all major computer platforms
• Support for multicore processors
• Support for GPU accelerated computation
• Many excellent VMD tutorials developed locally, and by the research community at large
• No limits on the number of molecules, atoms, residues or number of trajectory frames, except available memory