In the following, the value of $VMDDIR is the vmd installation directory. During the original installation this is the value of INSTALLLIBDIR. It can also be found by looking at the first few lines of the vmd startup script (head `which vmd`) or by starting VMD and using the command set env(VMDDIR).
As mentioned elsewhere, VMD uses the Tcl interpreter with two language extensions, TclX and Tcl-DP. Each of these three packages reads Tcl scripts at initialization, which are contained in VMD\ distribution; with a different directory for each package. The locations of the directories is determined by the environment variables defined in the vmd script. In order they are TCL_LIBRARY, TCLX_LIBRARY, and DP_LIBRARY, which are set in the vmd startup script to $VMDDIR/scripts/tcl, $VMDDIR/scripts/tclX, and $VMDDIR/scripts/dp, respectively. In addition, VMD has its own directory of core Tcl routines.
The most important of these is tt $VMDDIR/scripts/vmd/vmdinit.tcl. This file sets up the basic Tcl initialization commands including the commands that catch Ctrl-C interrupts, define some environment variables, and add the vmd script directory to the Tcl autoindex path. Most of the other files are referenced through the auto_path.
There are a few non-Tcl scripts in this directory. Currently these are perl scripts used for the urlload command and web client startup (see section § and section §).