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►Change Log
Version 2.0
Version 2.1
Version 2.2
Version 2.3
Version 2.4
Version 2.5
Version 2.6
Version 2.7
Version 2.8
Version 2.9
►Installation
►Code specific notes
gromacs-2020.7
gromacs-2021.7
gromacs-2022.5
gromacs-2023
namd-2.12
namd-2.13
namd-2.14
qespresso-5.0.2
qespresso-6.2
qespresso-7.0
qespresso-7.2
►Getting Started
UNITS
►Collective Variables
►Groups and Virtual Atoms
GROUP
MOLINFO
WHOLEMOLECULES
FIT_TO_TEMPLATE
WRAPAROUND
RESET_CELL
CENTER
CENTER_OF_MULTICOLVAR
COM
FIXEDATOM
GHOST
►CV Documentation
ADAPTIVE_PATH
ALPHABETA
ALPHARMSD
ANGLE
ANTIBETARMSD
CELL
CONSTANT
CONTACTMAP
COORDINATION
DHENERGY
DIHCOR
DIMER
DIPOLE
DISTANCE
DISTANCE_FROM_CONTOUR
EEFSOLV
ENERGY
ERMSD
EXTRACV
FAKE
GHBFIX
GPROPERTYMAP
GYRATION
PARABETARMSD
PATH
PATHMSD
PCAVARS
POSITION
PROJECTION_ON_AXIS
PROPERTYMAP
PUCKERING
TEMPLATE
TORSION
VOLUME
►Distances from reference configurations
DRMSD
MULTI_RMSD
PCARMSD
RMSD
TARGET
►Functions
COMBINE
►CUSTOM
TIME
ENSEMBLE
FUNCPATHGENERAL
FUNCPATHMSD
FUNCSUMHILLS
LOCALENSEMBLE
MATHEVAL
PIECEWISE
SORT
STATS
►MultiColvar
ANGLES
BOND_DIRECTIONS
BRIDGE
COORDINATIONNUMBER
DENSITY
DISTANCES
ENVIRONMENTSIMILARITY
FCCUBIC
HBPAMM_SH
INPLANEDISTANCES
MOLECULES
PLANES
Q3
Q4
Q6
SIMPLECUBIC
TETRAHEDRAL
TORSIONS
XANGLES
XDISTANCES
XYDISTANCES
XYTORSIONS
XZDISTANCES
XZTORSIONS
YANGLES
YDISTANCES
YXTORSIONS
YZDISTANCES
YZTORSIONS
ZANGLES
ZDISTANCES
ZXTORSIONS
ZYTORSIONS
MFILTER_BETWEEN
MFILTER_LESS
MFILTER_MORE
AROUND
CAVITY
INCYLINDER
INENVELOPE
INSPHERE
TETRAHEDRALPORE
GRADIENT
INTERMOLECULARTORSIONS
LOCAL_AVERAGE
LOCAL_Q3
LOCAL_Q4
LOCAL_Q6
MCOLV_COMBINE
MCOLV_PRODUCT
NLINKS
PAMM
POLYMER_ANGLES
SMAC
MTRANSFORM_BETWEEN
MTRANSFORM_LESS
MTRANSFORM_MORE
LWALLS
UWALLS
►Exploiting contact matrices
ALIGNED_MATRIX
CONTACT_MATRIX
HBOND_MATRIX
HBPAMM_MATRIX
SMAC_MATRIX
TOPOLOGY_MATRIX
CLUSTER_WITHSURFACE
COLUMNSUMS
DFSCLUSTERING
ROWSUMS
SPRINT
CLUSTER_DIAMETER
CLUSTER_DISTRIBUTION
CLUSTER_NATOMS
CLUSTER_PROPERTIES
DUMPGRAPH
OUTPUT_CLUSTER
►Analysis
COMMITTOR
DUMPATOMS
DUMPDERIVATIVES
DUMPFORCES
DUMPMASSCHARGE
DUMPMULTICOLVAR
DUMPPROJECTIONS
►PRINT
FLUSH
UPDATE_IF
REWEIGHT_BIAS
REWEIGHT_METAD
REWEIGHT_TEMP_PRESS
REWEIGHT_WHAM
WHAM_HISTOGRAM
WHAM_WEIGHTS
AVERAGE
HISTOGRAM
MULTICOLVARDENS
CONVERT_TO_FES
DUMPCUBE
DUMPGRID
FIND_CONTOUR
FIND_CONTOUR_SURFACE
FIND_SPHERICAL_CONTOUR
FOURIER_TRANSFORM
GRID_TO_XYZ
INTEGRATE_GRID
INTERPOLATE_GRID
COLLECT_FRAMES
EUCLIDEAN_DISSIMILARITIES
PRINT_DISSIMILARITY_MATRIX
READ_DISSIMILARITY_MATRIX
LANDMARK_SELECT_FPS
LANDMARK_SELECT_RANDOM
LANDMARK_SELECT_STAGED
LANDMARK_SELECT_STRIDE
RESELECT_LANDMARKS
CLASSICAL_MDS
OUTPUT_PCA_PROJECTION
PCA
PROJECT_ALL_ANALYSIS_DATA
SKETCHMAP_CONJGRAD
SKETCHMAP_POINTWISE
SKETCHMAP_READ
SKETCHMAP_SMACOF
SKETCH_MAP
SMACOF_MDS
OUTPUT_ANALYSIS_DATA_TO_COLVAR
OUTPUT_ANALYSIS_DATA_TO_PDB
►Bias
ABMD
BIASVALUE
EXTENDED_LAGRANGIAN
EXTERNAL
LOWER_WALLS
MAXENT
METAD
MOVINGRESTRAINT
PBMETAD
RESTRAINT
UPPER_WALLS
RESTART
►Additional Modules
►ANN (Artificial Neural Network) function
►Functions Documentation
ANN
►FISST (Infinite Switch Simulated Tempering in Force)
►Biases Documentation
FISST
►PLUMED-ISDB
►CVs Documentation
CS2BACKBONE
EMMI
FRET
JCOUPLING
NOE
PCS
PRE
RDC
SANS
SAXS
►Functions Documentation
SELECT
►General Actions Documentation
SELECTOR
►Biases Documentation
CALIBER
METAINFERENCE
RESCALE
►Tutorials
ISDB: setting up a Metadynamics Metainference simulation
ISDB: setting up a SAXS post processing and refinement calculation using MARTINI form factors
►PYTORCH (Machine Learning Collective Variables)
►Functions Documentation
PYTORCH_MODEL
►Logarithmic Mean Force Dynamics
►Biases Documentation
LOGMFD
►Experiment Directed Simulation
►Biases Documentation
EDS
►Extended-System Adaptive Biasing Force
►Biases Documentation
DRR
►Command Line Tools
drr_tool
►Variationally Enhanced Sampling (VES code)
►Biases
VES_DELTA_F
VES_LINEAR_EXPANSION
►Basis functions
BF_CHEBYSHEV
BF_COMBINED
BF_COSINE
BF_CUBIC_B_SPLINES
BF_CUSTOM
BF_FOURIER
BF_GAUSSIANS
BF_LEGENDRE
BF_POWERS
BF_SINE
BF_WAVELETS
►Target Distributions
TD_CHI
TD_CHISQUARED
TD_CUSTOM
TD_EXPONENTIAL
TD_EXPONENTIALLY_MODIFIED_GAUSSIAN
TD_GAUSSIAN
TD_GENERALIZED_EXTREME_VALUE
TD_GENERALIZED_NORMAL
TD_GRID
TD_LINEAR_COMBINATION
TD_MULTICANONICAL
TD_MULTITHERMAL_MULTIBARIC
TD_PRODUCT_COMBINATION
TD_PRODUCT_DISTRIBUTION
TD_UNIFORM
TD_VONMISES
TD_WELLTEMPERED
►Optimizers
OPT_ADAM
OPT_AVERAGED_SGD
OPT_DUMMY
OPT_ROBBINS_MONRO_SGD
►Utilities
VES_OUTPUT_BASISFUNCTIONS
VES_OUTPUT_FES
VES_OUTPUT_TARGET_DISTRIBUTION
►Command Line Tools
ves_md_linearexpansion
►Tutorials
MARVEL-VES School February 2017
MARVEL-VES tutorial (Lugano Feb 2017): Metadynamics
MARVEL-VES tutorial (Lugano Feb 2017): VES 1
MARVEL-VES tutorial (Lugano Feb 2017): VES 2
MARVEL-VES tutorial (Lugano Feb 2017): Kinetics
►MAZE
►Loss
MAZE_LOSS
►Optimizers
MAZE_MEMETIC_SAMPLING
MAZE_RANDOM_ACCELERATION_MD
MAZE_RANDOM_WALK
MAZE_SIMULATED_ANNEALING
MAZE_STEERED_MD
►Biases
MAZE_OPTIMIZER_BIAS
►OPES (On-the-fly Probability Enhanced Sampling)
►Biases
OPES_EXPANDED
OPES_METAD
OPES_METAD_EXPLORE
►Expansion Collective Variables
ECV_CUSTOM
ECV_LINEAR
ECV_MULTITHERMAL
ECV_MULTITHERMAL_MULTIBARIC
ECV_UMBRELLAS_FILE
ECV_UMBRELLAS_LINE
►Tutorials
PLUMED Masterclass 22.3 OPES method
OPES_METAD Tutorial: Running and post-processing
►PIV collective variable
►CVs Documentation
PIV
►S2 contact model collective variable
►CVs Documentation
S2CM
►SASA collective variable
►CVs Documentation
SASA_HASEL
SASA_LCPO
►Funnel-Metadynamics (FM)
►CV documentation
FUNNEL_PS
►Bias Documentation
FUNNEL
►Membrane Fusion
►CVs Documentation
FUSIONPOREEXPANSIONP
FUSIONPORENUCLEATIONP
MEMFUSIONP
►Command Line Tools
completion
config
►driver
READ
driver-float
gen_example
gen_json
gentemplate
info
kt
manual
mklib
newcv
partial_tempering
patch
pathtools
pdbrenumber
pesmd
selector
simplemd
sum_hills
vim2html
►Miscellaneous
►Comments
ENDPLUMED
Continuation lines
Using VIM syntax file
Using bash autocompletion
►Including other files
INCLUDE
►Loading shared libraries
LOAD
►Embed a separate PLUMED instance
PLUMED
►Debugging the code
DEBUG
►Changing exchange patterns in replica exchange
RANDOM_EXCHANGES
List of modules
Special replica syntax
Parsing constants
►Frequently used tools
histogrambead
kernelfunctions
pdbreader
switchingfunction
Regular Expressions
Files
►Tutorials
Master ISDD tutorial 2024: Brief introduction to PLUMED
Master ISDD tutorial 2024: Metadynamics simulations with PLUMED
PLUMED Masterclass 22.1: Funnel-Metadynamics
PLUMED Masterclass 22.2: Analysis of Plumed output by Metadynminer
PLUMED Masterclass 22.3: OPES method
PLUMED Masterclass 22.5: Machine learning collective variables with Pytorch
PLUMED Masterclass 22.6: EDS module + Coarse-Grained directed simulations
PLUMED Masterclass 22.8: Modelling Concentration-driven processes with PLUMED
PLUMED Masterclass 22.9: Using path collective variables to find reaction mechanisms in complex free energy landscapes
PLUMED Masterclass 22.10: Hamiltonian replica exchange with PLUMED and GROMACS
PLUMED Masterclass 22.11: Variationally enhanced sampling with PLUMED
PLUMED Masterclass 22.12: Liquid-solid chemical potential differences with the environment similarity CV
PLUMED Masterclass 22.13: SASA module and the application of PLUMED for implicit solvent simulations
PLUMED Masterclass 22.15: FISST module and application of mechanical forces with PLUMED
PLUMED Masterclass 21.1: PLUMED syntax and analysis
PLUMED Masterclass 21.2: Statistical errors in MD
PLUMED Masterclass 21.3: Umbrella sampling
PLUMED Masterclass 21.4: Metadynamics
PLUMED Masterclass 21.5: Simulations with multiple replicas
PLUMED Masterclass 21.6: Dimensionality reduction
PLUMED Masterclass 21.7: Optimizing PLUMED performances
Advanced Methods in MD 2023: Metadynamics simulations with PLUMED
Lugano tutorial: Brief guide to PLUMED syntax and analyzing trajectories
Lugano tutorial: Using restraints
Lugano tutorial: Metadynamics simulations with PLUMED
Lugano tutorial: Calculating error bars
Lugano tutorial: Dimensionality reduction
Lugano tutorial: Using PLUMED with LAMMPS
Lugano tutorial: Binding of a ion and a dinucleotide
Lugano tutorial: Computing proton transfer in water
Lugano tutorial: Folding free energy for a protein described by a go-model
Using Hamiltonian replica exchange with GROMACS
Julich tutorial: Developing CVs in plumed
ESDW Workshop Lyon 2019: A very simple introduction to PLUMED
MARVEL tutorial: Analyzing CVs
MARVEL tutorial: Path CVs
Optimizing PLUMED performance
►Old Tutorials
Trieste tutorial: Analyzing trajectories using PLUMED
Trieste tutorial: Averaging, histograms and block analysis
Trieste tutorial: Using restraints
Trieste tutorial: Metadynamics simulations with PLUMED
Trieste tutorial: Running and analyzing multi-replica simulations.
Trieste tutorial: Real-life applications with complex CVs
Belfast tutorial: Analyzing CVs
Belfast tutorial: Adaptive variables I
Belfast tutorial: Adaptive variables II
Belfast tutorial: Umbrella sampling
Belfast tutorial: Out of equilibrium dynamics
Belfast tutorial: Metadynamics
Belfast tutorial: Replica exchange I
Belfast tutorial: Replica exchange II and Multiple walkers
Belfast tutorial: NMR restraints
Belfast tutorial: Steinhardt Parameters
Cambridge tutorial
CINECA tutorial
Moving from PLUMED 1 to PLUMED 2
Munster tutorial
►Performances
GROMACS and PLUMED with GPU
Metadynamics
►Multiple time stepping
EFFECTIVE_ENERGY_DRIFT
Multicolvar
Neighbor Lists
OpenMP
Secondary Structure
Time your Input
Making lepton library faster
Index of Actions
Bug List
Todo List
Bibliography