Funnel ABF and Funnel Metadynamics#302
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gustavor101 wants to merge 28 commits intoSSAGESLabs:mainfrom
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Add the funnel Metadynamics and Funnel ABF along with the restraint function
Add the funnel collective variable
Add the loggers for the funnel methods
add funnel_cv in the list of collective variables
Add funnel examples
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Merging to
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Activate cv restraints
Make restrains functional on every range of cv_max
Add perpendicular projection as CV
Reduce number of functions in funnel function
Correct restraint bias shape.
Add spectral abf with external restraints
add spectral abf with external restraints
remove unused variables
remove duplicated force calculation
Funnel ABF has now the option of different solvers like ABF and the analyze is more stable. This comit prepare the branch for restraints in FUNN and CFF.
This commit solves the issue with old funnel abf pickle files, it will be removed in future updates.
Time dependent restraints for reaction pathways discovery.
Add Nanoreactor method
Initial commit for funnel metad with abf support
Add funnel metadynamics method with force decomposition of the restraint. Bias is driven by metadynamics and analysis done with ABF.
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Implementation of Funnel Metadynamics (https://doi.org/10.1073/pnas.1303186110) and the Funnel ABF version following the ABF implementation of PMFLib - A Toolkit for Free Energy Calculations (https://pmflib.ncbr.muni.cz/).