Syntax changes from older versions

The following is a list of syntax changes in Colvars since its first release. Many of the older keywords are still recognized by the current code, thanks to specific compatibility code. This is not a list of new features: its primary purpose is to make you aware of those improvements that affect the use of old configuration files with new versions of the code.

Note: if you are using any of the NAMD and VMD tutorials:
https://www.ks.uiuc.edu/Training/Tutorials/
please be aware that several of these tutorials are not actively maintained: for those cases, this list will help you reconcile any inconsistencies.

• Colvars version 2016-06-09 or later (NAMD version 2.12b1 or later).
  The legacy keyword refPositionsGroup has been renamed fittingGroup (see 9.4.2) for clarity (the legacy version is still supported).

• Colvars version 2016-08-10 or later (NAMD version 2.12b1 or later).
  ``System forces'' have been replaced by ``total forces'' (see for example outputTotalForce (see 9.3.9)). See the following page for more information:
  https://colvars.github.io/README-totalforce.html

• Colvars version 2017-01-09 or later (NAMD version 2.13b1 or later).
  A new type of restraint, harmonicWalls (see 9.5.6), replaces and improves upon the legacy keywords lowerWall and upperWall: these are still supported as short-hands.

• Deprecation warning for calculations including wall potentials.
  The legacy keywords lowerWall and upperWall will stop having default values and will need to be set explicitly (preferably as part of the harmonicWalls restraint). When using an ABF bias, it is recommended to set the two walls equal to lowerBoundary (see 9.3.8) and upperBoundary (see 9.3.8), respectively. When using a metadynamics bias, it is recommended to set the two walls within lowerBoundary (see 9.3.8) and upperBoundary (see 9.3.8). This guarantees that the tails of each Gaussian hill are accounted in the region between the grid boundaries and the wall potentials. See also expandBoundaries (see 9.3.8) for an automatic definition of the PMF grid boundaries.

Up-to-date documentation can always be accessed at:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html