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@@ -5,9 +5,9 @@ This directory contains both standalone tools and Colvars scripts.
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## Standalone tools
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| File name | Summary |
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| ------------- | ------------- |
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|**abf_integrate**|Process free energy gradient from ABF/TI to generate a free energy surface using a legacy MCMC procedure. Superseded by Poisson integration (builtin or standalone) for dimensions 2 and 3, still needed for higher-dimension PMFs. Build using the provided **Makefile**.|
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|**poisson_integrator**| Process free energy gradient from ABF/TI to generate a free energy surface as the solution of a Poisson equation. Build using the provided **Makefile**.|
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|**poisson_integrator_conv**| Process free energy gradient from ABF/TI to generate a free energy surface as the solution of a Poisson equation, monitoring convergence towards a given discretized scalar field. Build using the provided **Makefile**.|
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|**abf_integrate**|Legacy tool to process free energy gradient from ABF/TI to generate a free energy surface using a legacy MCMC procedure. Superseded by Poisson integration (builtin or standalone) for dimensions 2 and 3, still needed for higher-dimension PMFs. Build using the provided Makefile.|
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|**poisson_integrator**| Process free energy gradient from ABF/TI to generate a free energy surface as the solution of a Poisson equation. Build using cmake.|
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|**poisson_integrator_conv**| Process free energy gradient from ABF/TI to generate a free energy surface as the solution of a Poisson equation, monitoring convergence towards a given discretized scalar field. Build using cmake.|
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|**noe_to_colvars.py**| Parse an X-PLOR style list of assign commands for NOE restraints.|
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|**plot_colvars_traj.py**| Select variables from a Colvars trajectory file and optionally plot them as a 1D graph as a function of time or of one of the variables.|
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