Additional Modules

Here is collected the documentation for the additional modules contributed to PLUMED. For information on how to enable modules see List of modules.

ModuleDescriptionAuthors

References

ANN (Artificial Neural Network) function ANN (Artificial Neural Network) function Wei Chen and Andrew Ferguson
FISST (Infinite Switch Simulated Tempering in Force) Infinite Switch Simulated Tempering in Force (FISST) Glen Hocky [56]
PLUMED-ISDB Integrative Structural and Dynamical Biology with PLUMED Max Bonomi and Carlo Camilloni [15]
Logarithmic Mean Force Dynamics Method for enhanced sampling and for free energy calculations along collective variables Tetsuya Morishita, Naoki Watanabe [80] [81] [82]
Experiment Directed Simulation Methods for incorporating additional information about CVs into MD simulations by adaptively determined linear bias parameters Glen Hocky, Andrew White [123] [57] [2]
Extended-System Adaptive Biasing Force Methods for performing eABF or DRR method to calculate PMF along CVs Haochuan Chen, Haohao Fu [37] [70] [71] [47]
Variationally Enhanced Sampling (VES code) Module that implements enhanced sampling methods based on Variationally Enhanced Sampling Omar Valsson [117]
MAZE Module that implements enhanced sampling methods for ligand unbinding from protein tunnels Jakub Rydzewski [101]
OPES (On-the-fly Probability Enhanced Sampling) On-the-fly Probability Enhanced Sampling (OPES) Michele Invernizzi [62]
PIV collective variable Permutation invariant collective variable (PIV) S. Pipolo, F. Pietrucci [48] [95]
Funnel-Metadynamics (FM) a collective variable and a bias action necessary to perform Funnel-Metadynamics on Molecular Dynamics simulations Stefano Raniolo, Vittorio Limongelli

[72] [99]