After initialization is complete, VMD reads the startup file. This file contains text commands for VMD to execute, just as if they had been entered at the VMD text console command prompt. The file can contain any number of commands, including blank lines and comment lines (which begin with the # character). If an error is encountered while reading this file, the command in error is skipped and processing of the file continues.
The base filename for this startup file is .vmdrc by default on Unix systems and vmd.rc on Windows; this is determined by the configuration parameter STARTUPFILENAME. VMD searches for this file in a number of locations, and reads in the first version of the file it finds. The order of searching for the file is: