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  ``System forces'' have been replaced by ``total forces'' (see for example outputTotalForce (see 9.3.19)). 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 9.5.7), replaces and improves upon the legacy keywords lowerWall and upperWall: these are still supported as short-hands.

• Colvars version 2018-11-15 or later (NAMD version 2.14b1 or later).
  The global analysis keyword has been discontinued: specific analysis tasks are controlled directly by the keywords corrFunc (see 9.3.23) and runAve (see 9.3.23), which continue to remain off by default.

• Colvars version 2020-02-25 or later (NAMD version 2.14b1 or later).
  The parameter hillWidth (see 9.5.4), expressing the Gaussian width $2\sigma$ in relative units (number of grid points), does not have a default value any more. A new alternative parameter gaussianSigmas (see 9.5.4) allows setting the $\sigma$ parameters explicitly for each variable if needed.
  Furthermore, to facilitate the use of other analysis tools such as for example sum_hills:
  https://www.plumed.org/doc-v2.6/user-doc/html/sum_hills.html
  the format of the file written by writeHillsTrajectory (see 9.5.4) has also been changed to use $\sigma$ instead of $2\sigma$ . This change does not affect how the biasing potential is written in the state file, or the simulated trajectory.

• Colvars version 2020-02-25 or later (NAMD version 2.14b1 or later).
  The legacy keywords lowerWall and upperWall of a colvar definition block do not have default values any longer, and 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 9.3.18) and upperBoundary (see 9.3.18), respectively. When using a metadynamics bias, it is recommended to set the two walls strictly within lowerBoundary (see 9.3.18) and upperBoundary (see 9.3.18); see 9.5.4 for details.

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