Once all parameters have been properly specified, the configure script must be run to create a Makefile for compiling and installing VMD. This Makefile is copied into the src and doc directories. The syntax for running the configure script is:
configure [<OSTYPE> [OPT1 [OPT2 ...]]]where <OSTYPE> is a keyword specifying one of the operating systems mentioned below, and OPT1, OPT2, ... are keywords specifying which optional VMD components should be included when the program is compiled and linked. The total possible optional keywords are explained below. When multiple options are specified and the list contains contradictory options, the last value specified in the command is used. Each time configure is run, a copy of the list of parameters used is written to the file configure.options; if simply the command
configureis run, the values contained in configure.options will be used as the arguments. In this way, when a ``default'' configuration has been established previously, and a new Makefile must be generated for some reason, the user need only go to the main VMD working directory and type configure. The file configure.options may be edited by hand to set the list of options to the required values, after which the user may simply type configure.