From Bioinformatics.Org Wiki
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. It is one of the most user-friendly programs available for this purpose. It is particularly useful for visualizing trajectories, either, e.g., in Charmm (.DCD) or PDB (MODEL ... ENDMDL) formats.
- To vizualize a trajectory, do:
- vmd structure.pdb
- In the "VMD main" window, select your molecule.
- In the File menue, select "Load data into Molecule"
- Browse and select your trajectory file
- If it is not recognized automatically, you may have to specify the correct file format
- To animate your structure, click on the arrow at the bottom-right of the "VMD main" window
- To generate a Charmm trajectory (.DCD) from a series of PDB files, you may use Catdcd as follows:
- cat *.pdb > file_all.pdb
- catdcd -o file_all.dcd -pdb file_all.pdb
- NAMD - NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.