A great resource is the user manual .
One can run scripts in VMD command line (example scripts).
To run a script (in windows) type source in the command line followed by the fill name.
Useful atom selection commands:
"within <distance> of <selection>" "same <property> as <selection>" same resid as within 5 of resname LIG
here is a script to calculate rmsd's: vmd.rmsd.csh.