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►Change Log
Version 2.0
Version 2.1
Version 2.10
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-2022.5
gromacs-2023.5
gromacs-2024.3
gromacs-2025.0
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
ARGS2VATOM
CENTER
CENTER_FAST
COM
FIXEDATOM
GHOST
►CV Documentation
ADAPTIVE_PATH
ALPHARMSD
ANGLE
ANGLES
ANGLE_SCALAR
ANGLE_VECTOR
ANTIBETARMSD
BETWEEN_MATRIX
BOPS
CELL
COMBINE_MATRIX
CONSTANT
CONTACTMAP
COORDINATION
CUSTOM_MATRIX
DHENERGY
DIHCOR
DIHEDRAL_CORRELATION
DIHEDRAL_CORRELATION_SCALAR
DIHEDRAL_CORRELATION_VECTOR
DIMER
DIPOLE
DIPOLE_SCALAR
DISTANCE
DISTANCE_FROM_CONTOUR
DISTANCE_FROM_SPHERICAL_CONTOUR
DOPS
EEFSOLV
ENERGY
ERMSD
EXTRACV
FAKE
GEOMETRIC_PATH
GHBFIX
GPATH
GPROPERTYMAP
GSYMFUNC_THREEBODY
GYRATION
GYRATION_FAST
HBPAMM_SA
HBPAMM_SD
HBPAMM_SH
HIGHEST_SCALAR
HIGHEST_VECTOR
LESS_THAN_MATRIX
LOWEST_SCALAR
LOWEST_VECTOR
MATHEVAL_MATRIX
MEAN
MEAN_SCALAR
MEAN_VECTOR
MORE_THAN_MATRIX
ONES
OUTER_PRODUCT
PARABETARMSD
PATH
PATHMSD
PCAVARS
PDB2CONSTANT
PLANE
PLANE_SCALAR
PLANE_VECTOR
POSITION
POSITION_SCALAR
POSITION_VECTOR
PROJECTION_ON_AXIS
PROPERTYMAP
PUCKERING
QUATERNION
QUATERNION_SCALAR
QUATERNION_VECTOR
READMASSCHARGE
ROPS
SUM
SUM_MATRIX
SUM_SCALAR
SUM_VECTOR
TEMPLATE
TORSION
TORSION_SCALAR
VOLUME
XANGLES
XYTORSIONS
XZTORSIONS
YANGLES
YXTORSIONS
YZTORSIONS
ZANGLES
ZXTORSIONS
ZYTORSIONS
►Distances from reference configurations
DRMSD
MULTI_RMSD
PCARMSD
RMSD
RMSD_SCALAR
RMSD_VECTOR
►Functions
BESSEL
BESSEL_SCALAR
BESSEL_VECTOR
BETWEEN
BETWEEN_VECTOR
COMBINE
COMBINE_SCALAR
COMBINE_VECTOR
►CUSTOM
TIME
CUSTOM_SCALAR
CUSTOM_VECTOR
DIFFERENCE
DIFFERENCE_SCALAR
DIFFERENCE_VECTOR
ENSEMBLE
FLATTEN
FUNCPATHGENERAL
FUNCPATHMSD
FUNCSUMHILLS
HIGHEST
KERNEL
LESS_THAN
LESS_THAN_VECTOR
LOCALENSEMBLE
LOWEST
MAHALANOBIS_DISTANCE
MATHEVAL
MATHEVAL_SCALAR
MATHEVAL_VECTOR
MATRIX_PRODUCT_DIAGONAL
MOMENTS
MOMENTS_SCALAR
MOMENTS_VECTOR
MORE_THAN
MORE_THAN_VECTOR
NORMALIZED_EUCLIDEAN_DISTANCE
PIECEWISE
PIECEWISE_SCALAR
PRODUCT
SORT
SORT_SCALAR
SORT_VECTOR
STATS
►MultiColvar
ALPHABETA
AROUND_CALC
ATOMIC_SMAC
BRIDGE
BRIDGE_MATRIX
CAVITY_CALC
CHARGE
CHARGE_SCALAR
CHARGE_VECTOR
CONCATENATE
COORDINATIONNUMBER
COORDINATION_MOMENTS
COORDINATION_SHELL_AVERAGE
COORDINATION_SHELL_FUNCTION
COORD_ANGLES
CYLINDRICAL_HARMONIC
CYLINDRICAL_HARMONIC_MATRIX
DENSITY
DETERMINANT
DIPOLE_VECTOR
DISPLACEMENT
DISTANCES
DISTANCE_SCALAR
DISTANCE_VECTOR
DUMPMULTICOLVAR
ENVIRONMENTSIMILARITY
EUCLIDEAN_DISTANCE
FCCUBIC
FCCUBIC_FUNC
FCCUBIC_FUNC_MATRIX
GRADIENT
GYRATION_TENSOR
HEXACTIC_PARAMETER
INCYLINDER_CALC
INPLANEDISTANCES
INSPHERE_CALC
INVERT_MATRIX
LOCAL_CRYSTALINITY
MASS
MASS_SCALAR
MASS_VECTOR
MATRIX_PRODUCT
MATRIX_VECTOR_PRODUCT
MFILTER_LESS
MFILTER_MORE
NEIGHBORS
PAIRENTROPIES
PAIRENTROPY
PLANES
Q1
Q3
Q4
Q6
QUATERNION_BOND_PRODUCT_MATRIX
QUATERNION_PRODUCT_MATRIX
SECONDARY_STRUCTURE_RMSD
SIMPLECUBIC
SMAC
SPHERICAL_HARMONIC
SPHERICAL_HARMONIC_MATRIX
TETRAHEDRAL
TETRAHEDRALPORE_CALC
TETRA_ANGULAR
TETRA_RADIAL
TORSIONS
TORSIONS_MATRIX
TORSION_VECTOR
TRANSPOSE
UWALLS
VORONOI
VSTACK
XDISTANCES
YDISTANCES
ZDISTANCES
AROUND
CAVITY
INCYLINDER
INENVELOPE
INENVELOPE_CALC
INSPHERE
TETRAHEDRALPORE
LOCAL_AVERAGE
LOCAL_Q1
LOCAL_Q3
LOCAL_Q4
LOCAL_Q6
PAMM
►Exploiting contact matrices
CONTACT_MATRIX
CONTACT_MATRIX_PROPER
DISTANCE_MATRIX
HBOND_MATRIX
HBPAMM_MATRIX
TOPOLOGY_MATRIX
DFSCLUSTERING
SPRINT
CLUSTER_DIAMETER
CLUSTER_DISTRIBUTION
CLUSTER_DISTRIBUTION_CALC
CLUSTER_NATOMS
CLUSTER_PROPERTIES
CLUSTER_WEIGHTS
CLUSTER_WITHSURFACE
OUTPUT_CLUSTER
►Analysis
COMMITTOR
DUMPATOMS
DUMPDERIVATIVES
DUMPFORCES
DUMPMASSCHARGE
DUMPPDB
DUMPPROJECTIONS
DUMPVECTOR
►PRINT
FLUSH
PRINT_NDX
SELECT_COMPONENTS
SELECT_WITH_MASK
UPDATE_IF
COVARIANCE_MATRIX
REWEIGHT_BIAS
REWEIGHT_METAD
REWEIGHT_TEMP_PRESS
WHAM
WHAM_HISTOGRAM
WHAM_WEIGHTS
ACCUMULATE
AVERAGE
CUSTOM_GRID
EVALUATE_FUNCTION_FROM_GRID
EVALUATE_FUNCTION_FROM_GRID_SCALAR
EVALUATE_FUNCTION_FROM_GRID_VECTOR
FIND_GRID_MAXIMUM
FIND_GRID_MINIMUM
HISTOGRAM
INTEGRATE_GRID
MATHEVAL_GRID
MULTICOLVARDENS
REFERENCE_GRID
SUM_GRID
CONVERT_TO_FES
DUMPCONTOUR
DUMPCUBE
DUMPGRID
FIND_CONTOUR
FIND_CONTOUR_SURFACE
FIND_SPHERICAL_CONTOUR
FOURIER_TRANSFORM
INTERPOLATE_GRID
COLLECT_FRAMES
FARTHEST_POINT_SAMPLING
LANDMARK_SELECT_FPS
LANDMARK_SELECT_RANDOM
LANDMARK_SELECT_STRIDE
ARRANGE_POINTS
CLASSICAL_MDS
CREATE_MASK
PCA
PROJECT_POINTS
SKETCHMAP
SKETCHMAP_PROJECTION
►Bias
ABMD
BIASVALUE
EXTENDED_LAGRANGIAN
EXTERNAL
LOWER_WALLS
LOWER_WALLS_SCALAR
MAXENT
METAD
MOVINGRESTRAINT
PBMETAD
RESTRAINT
RESTRAINT_SCALAR
UPPER_WALLS
UPPER_WALLS_SCALAR
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
BAIES
CS2BACKBONE
EMMI
EMMIVOX
FRET
JCOUPLING
NOE
PCS
PRE
RDC
SANS
SAXS
SHADOW
►Functions Documentation
SELECT
►General Actions Documentation
SELECTOR
►Biases Documentation
CALIBER
METAINFERENCE
RESCALE
Tutorials
►sizeshape collective variable
CVs Documentation
►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
►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
►PIV collective variable
►CVs Documentation
PIV
►PYTORCH
►Functions Documentation
PYTORCH_MODEL
►S2 contact model collective variable
►CVs Documentation
S2CM
►SASA collective variable
►CVs Documentation
SASA_HASEL
SASA_LCPO
►Metatomic
METATOMIC
►Funnel-Metadynamics (FM)
►CV documentation
FUNNEL_PS
►Bias Documentation
FUNNEL
►Membrane Fusion
►CVs Documentation
FUSIONPOREEXPANSIONP
FUSIONPORENUCLEATIONP
MEMFUSIONP
►Command Line Tools
benchmark
completion
config
►driver
READ
driver-float
gen_example
gen_json
gentemplate
info
kt
manual
mklib
newcv
partial_tempering
patch
pathtools
pdbrenumber
pesmd
plotswitch
selector
show_graph
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
►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
AVERAGE_PATH_DISPLACEMENT
COLLECT
DIAGONALIZE
DISSIMILARITIES
DOMAIN_DECOMPOSITION
GATHER_REPLICAS
GET
KDE
KL_ENTROPY
LOGSUMEXP
PBC
PUT
RDF
REPARAMETERIZE_PATH
SIZESHAPE_POSITION_LINEAR_PROJ
SIZESHAPE_POSITION_MAHA_DIST
SPHERICAL_KDE
Bug List
Todo List
Bibliography