Configuration syntax used by the Colvars module

The Colvars configuration is usually read using the commands cv configfile (with a filename as argument) or cv config (with the configuration as a string argument). Each configuration line follows the format ``keyword value'', where the keyword and its value are separated by any white space. The following rules apply:

• keywords are case-insensitive (upperBoundary is the same as upperboundary and UPPERBOUNDARY): their string values are however case-sensitive (e.g. file names);

• a long value, or a list of multiple values, can be distributed across multiple lines by using curly braces, ``{'' and ``}'': the opening brace ``{'' must occur on the same line as the keyword, following a space character or other white space; the closing brace ``}'' can be at any position after that; any keywords following the closing brace on the same line are not valid (they should appear instead on a different line);

• many keywords are nested, and are only meaningful within a specific context: for every keyword documented in the following, the ``parent'' keyword that defines such context is also indicated;

• Tcl syntax is generally not available, but it is possible to use Tcl variables or bracket expansion of commands within a configuration string, when this is passed via the command cv config ...: for example, it is possible to convert the atom selection $sel into an atom group (see ) using cv config "atomNumbers { [$sel get serial] }";

• if a keyword requiring a boolean value (yes|on|true or no|off|false) is provided without an explicit value, it defaults to `yes|on|true'; for example, `outputAppliedForce' may be used as shorthand for `outputAppliedForce on';

• the hash character # indicates a comment: all text in the same line following this character will be ignored.