Here is collected the documentation for the additional modules contributed to PLUMED. For information on how to enable modules see List of modules.
Module | Description | Authors | References |
ANN (Artificial Neural Network) function | ANN (Artificial Neural Network) function | Wei Chen and Andrew Ferguson | |
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 | [76] [77] [78] |
MAZE | Method for enhanced sampling and for free energy calculations along collective variables | Tetsuya Morishita, Naoki Watanabe | [76] [77] [78] |
Experiment Directed Simulation | Methods for incorporating additional information about CVs into MD simulations by adaptively determined linear bias parameters | Glen Hocky, Andrew White | [116] [56] [2] |
Extended-System Adaptive Biasing Force | Methods for performing eABF or DRR method to calculate PMF along CVs | Haochuan Chen, Haohao Fu | [37] [67] [68] [47] |
Variationally Enhanced Sampling (VES code) | Module that implements enhanced sampling methods based on Variationally Enhanced Sampling | Omar Valsson | [110] |
PIV collective variable | Permutation invariant collective variable (PIV) | S. Pipolo, F. Pietrucci |