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The documentation of each individual command line tool is quite good. The documentation I think is lacking is the picking the right tool to get something done.
Something like having a page in the docs listing the commands which relate to each functionality bullet point;
- EVB mapping and automatic fitting of off-diagonal and gas shift parameters.
- Support for quantum classical path and group exclusion calculations.
- Linear response approximation (LRA) calculations (including group contributions)
- Parameter conversions (OPLS, Amber/GAFF).
or under some headings like - file conversion
- simulation setup
- analysis tools
This would make it a lot easier work out which of the commands to use for a particular task.
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