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 | |
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 |