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[detail level 1234]

▶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
▶Installation
▶Code specific notes
gromacs-2019.6
gromacs-2020.6
gromacs-2021.4
gromacs-4.5.7
namd-2.12
namd-2.13
namd-2.14
qespresso-5.0.2
qespresso-6.2
▶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
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
▶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
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
▶Command Line Tools
completion
config
▶driver
READ
driver-float
gen_example
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 2021: Brief introduction to PLUMED
Master ISDD tutorial 2021: Metadynamics simulations 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
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
Todo List
Bug List
Bibliography