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Bias-exchange metadynamics implementation #734

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This PR contains an implementation of bias-exchange metadynamics (https://doi.org/10.1021/jp067873l) based on the NAMD Tcl scripting interface.

Although most of the code is Tcl, the following significant changes are introduced to the C++ source code:

  • The value of the "active" flag of the biases is being written to the state file; this is needed because all biases are defined for all replicas, but only one is active at a time. Therefore, we need to carry over the active flag when checkpointing.
  • The value of the "active" flag can be reported on the trajectory.
  • The field name is now a member of colvardeps, and could later be moved to the AST (see [RFC] More band-aid fixes to Colvars #700 (comment) and related comments).
  • Allow updating and reporting in the scripting calls the energy and forces of a bias, but without actually sending those (used to decide the exchanges).
  • Adds a neutral bias, which simplifies greatly the inclusion of replicas with equilibrium sampling in the BE implementation.

@giacomofiorin giacomofiorin added NAMD script_API Control Colvars from scripts labels Oct 18, 2024
giacomofiorin and others added 28 commits October 18, 2024 13:47
…r now)

Started with the "active" flag, which is the most prominent example of a
feature that is not being set from the configuration file.
This prevents an error that would otherwise be raised due to the computed
value being inconsistent with the value from the state file (because the
latter was out of date when the state file was written).
Using this new feature to track the status of biases in BE-MTD
…ectory sorted by time

at constant bias, histograms are now optional
@giacomofiorin giacomofiorin modified the milestones: NAMD 3.1, GROMACS 2025 Oct 19, 2024
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