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During a simulation with collective variables defined, the following three output files are written:
- a state file, named outputName.colvars.state; this file is in ASCII format;
- if the parameter colvarsRestartFrequency is larger than zero, a restart file named restartName.colvars.state is written every that many steps: this file is equivalent to the final state file;
- if the parameter colvarsTrajFrequency is greater than 0 (default: 100), a trajectory file is written during the simulation: its name is outputName.colvars.traj; unlike the state file, it is not needed to restart a simulation, but can be used later for post-processing and analysis.
Other output files may be written by specific methods applied to the colvars (e.g. by the ABF method, see 13.5.1, or the metadynamics method, see 13.5.3).
Like the colvar trajectory file, they are needed only for analyzing, not continuing a simulation.
All such files' names also begin with the prefix outputName.