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.
Beyond the core capabilities of VMD , several additional features may be selectively included or excluded from the program by specifying the proper keywords to the configure script and then recompiling. As well, for some core features of VMD , a single value from a list of several possible options must be selected. This helps reduce the size of the resulting executable for users who have no need for certain options, and allows VMD to be compiled on architectures for which certain options are not available (due, for example, to a missing library or a hardware limitation). The following arguments to the configure script select these optional components; where multiple names are given in a list separated by `or' symbols ( |), only ONE of the items in that list should be given.
This option determines which 3D graphics rendering library to use. GL indicates to use the GL library (note, this does NOT mean OpenGL, it means GL); this option should be used on Silicon Graphics workstations. STARBASE indicates to use the HP Starbase library, and may be used on HP workstations (note that if STARBASE is specified, at present only a very limited graphical user interface will be available). Finally, if for some (strange) reason no graphics capabilities are desired in the program at all (perhaps if VMD is to be compiled to act only as a filter between PDB files and image files), NOGRAPHICS indicates to not include any graphics display capabilities at all.
This option determines which GUI library should be used by VMD , if any. VMD uses several separate user interface components, including the text console interface and the graphical user interface (GUI). FORMS indicates to use the Forms library of Mark Overmars; this option should be used when the GL library is used for the graphics, since Forms requires used of the GL library. TK indicates to use the Tk toolkit for the GUI; this option should be used when the STARBASE option is used for the graphics rendering library. (NOTE: the TK option is still very much in development, so FORMS should be used if at all possible. Also, TK requires that the Tk library already be installed on your system.) If no GUI is possible or desired, specifying NOGUI will not include any GUI library at all in VMD , and all VMD actions will have to be performed via text commands.
Tcl is a script parser and interpreter language which provides the capability to have interpreted scripts including control loops, variable substitution, function and procedure calls, and many other features. If the Tcl library is installed already on your system, VMD can use this library to parse and interpret text command scripts. Specifying the TCL option configures VMD to compile with this feature. If the Tcl library is not available on your system, NOTCL should be specified, which indicates for VMD to parse all text commands itself.
This option specifies to include (exclude) the capability to display and control molecular dynamics simulations running on remote supercomputers or workstations. This is a key feature for VMD , and the inclusion of this option is strongly encouraged. However, the option to exclude it from the final executable is available for users who have no need or interest in directly visualizing molecular dynamics simulations, or who wish to use VMD for some other preferred visualization feature. The REMOTE option requires use of the MDComm library, which must be available in the lib directory for the target operating system.
Indicates to have VMD use (or not use) the Tracker library developed at the University of North Carolina, Chapel Hill to access external 3D pointer devices. If UNC is specified, the UNC Tracker library will be linked with VMD , and the program will be able to use external spatial tracking devices such as a Polhemus Fastrak as a 3D pointer. Combined with some form of 3D display equipment such as a stereo projector, this provides a complete 3D environment for one or possibly several researchers. However, such equipment is not available for all users, and the Tracker library is not available on all OS types, so support for using the UNC library may be omitted.
The CAVE is a 3D display environment developed by the Electronic Visualization Laboratory at the University of Illinois at Chicago. VMD supports the use of the CAVE as a display device; VMD also supports the use of a CAVE-controlled spatial tracker as an input/control device when the CAVE is used for graphical display (similar, but distinct from, the use of the UNC Tracker library for working with other spatial tracking equipment). If the CAVE option is specified, VMD will include the capability to display molecules in a CAVE, and will link with the CAVE library which must be available in the lib directory for the target operating system. Some notes about the CAVE option:
An experimental capability of VMD is to use an external program for generation of text commands, which are then sent via PVM routines to VMD for execution. The EXTERNAL option enables this capability, and requires that PVM 3.3 or more recent be installed on your system. It is suggested not to use this option unless you know what you're doing.
VMD optionally may contain specific code to print debugging messages to the console during execution, for testing and development. If this code is included (by specifying the DEBUG option), user commands are available to turn on or off the printing of these messages, and to set the level of detail for the debugging output. However, VMD runs excruciatingly slow when this debugging code is included, so it is recommended to exclude it unless a specific problem is encountered that requires debugging output. By default, the DEBUG option is turned off, and the debugging code in VMD is commented out when the program is compiled. This option is mutually exclusive with the OPTIMIZE option described next. Including the DEBUG option also indicates to use the -g flag to the compiler to include necessary symbolic debugger information.
If OPTIMIZE is specified, all files are compiled with the -O optimization flag. If it is not specified, all files will be compiled with the -g flag, which includes symbolic debugger data in the executable. OPTIMIZE is mutually exclusive with the DEBUG option.
After configuration is complete, and a new Makefile has been generated and copied to the proper directories, the configure script will change to the src directory and execute a ``make'' command if directed. If this is done, no files are checked out, only a recompilation is done. If MAKE is specified, this automatic execution of a make command is done; if NOMAKE is specified, the make command is not executed, instead a warning message is issued and the configuration script completes.
Determines whether make commands are echoed to the screen as they are executed ( NOSILENT), or whether they are hidden ( SILENT).
Same as GL FORMS TCL REMOTE CAVE UNC OPTIMIZE.
Currently, VMD may be compiled on the following operating systems (the corresponding value for <OSTYPE> for the configure script is given in parentheses):