How do I display molecular dynamics trajectories with VMD?
VMD can read molecular trajectories from XPlor/CHARMm DCD files, Amber CRD files, a set of PDB files, or from a running molecular dynamics program. If your dynamics output is already in DCD format, then with the “Mol” form, choose “Load Molecule” to directly load this DCD file along with its corresponding PSF or PDB specification. A similar option is available for reading an Amber structure along with its CRD file. The “Animate” form can then be used to playback the simulation. If you have a collection of PDB files, or a hybrid set of PDB and DCD files, then you will want to open the “Edit Animation” form. With this menu you can read in new coordinates to be appended to the end of the stored animation list for a selected molecule. This same form can be used to write out parts of the animation in DCD, CRD or PDB format. This is a useful option for merging trajectory files or exporting single frames of a given simulation. Please see the VMD User’s Guide for detailed instructions regardin
