Index

A

AbstractMiddleRespaIntegrator (class in ufedmm.integrators) add_inner_nonbonded_force() (in module ufedmm.integrators) add_periodic_task() (ufedmm.ufedmm.ExtendedSpaceSimulation method)

AlanineDipeptideModel (class in ufedmm.testmodels) analysis module Analyzer (class in ufedmm.analysis)

C

centers_and_mean_forces() (ufedmm.analysis.FreeEnergyAnalyzer method)

CollectiveVariable (class in ufedmm.ufedmm) CustomIntegrator (class in ufedmm.integrators)

D

deserialize() (in module ufedmm.io)

DynamicalVariable (class in ufedmm.ufedmm)

E

effective_mass() (ufedmm.ufedmm.CollectiveVariable method) evaluate() (ufedmm.ufedmm.CollectiveVariable method) (ufedmm.ufedmm.DynamicalVariable method)

ExtendedSpaceContext (class in ufedmm.ufedmm) ExtendedSpaceSimulation (class in ufedmm.ufedmm) ExtendedSpaceState (class in ufedmm.ufedmm)

F

free_energy_functions() (ufedmm.analysis.Analyzer method)

FreeEnergyAnalyzer (class in ufedmm.analysis)

G

GeodesicLangevinIntegrator (class in ufedmm.integrators) getDynamicalVariables() (ufedmm.ufedmm.ExtendedSpaceState method)

getPositions() (ufedmm.ufedmm.ExtendedSpaceState method) getState() (ufedmm.ufedmm.ExtendedSpaceContext method) getVelocities() (ufedmm.ufedmm.ExtendedSpaceState method)

I

integrators module

io module

L

loadCheckpoint() (ufedmm.ufedmm.ExtendedSpaceSimulation method)

M

mean_force_free_energy() (ufedmm.analysis.FreeEnergyAnalyzer method) metadynamics_bias_free_energy() (ufedmm.analysis.FreeEnergyAnalyzer method) MiddleMassiveGGMTIntegrator (class in ufedmm.integrators) MiddleMassiveNHCIntegrator (class in ufedmm.integrators) module analysis integrators io testmodels ufedmm ufedmm.analysis ufedmm.integrators ufedmm.io ufedmm.testmodels ufedmm.ufedmm

N

NHC

O

ODE

R

RegulatedNHLIntegrator (class in ufedmm.integrators)

S

saveCheckpoint() (ufedmm.ufedmm.ExtendedSpaceSimulation method) SDE serialize() (in module ufedmm.io) setPeriodicBoxVectors() (ufedmm.ufedmm.ExtendedSpaceContext method) setPositions() (ufedmm.ufedmm.ExtendedSpaceContext method)

setVelocitiesToTemperature() (ufedmm.ufedmm.ExtendedSpaceContext method) simulation() (ufedmm.ufedmm.UnifiedFreeEnergyDynamics method) StateDataReporter (class in ufedmm.io) step() (ufedmm.integrators.CustomIntegrator method) (ufedmm.ufedmm.ExtendedSpaceSimulation method)

T

Tee (class in ufedmm.io)

testmodels module

U

UFED ufedmm module ufedmm.analysis module ufedmm.integrators module

ufedmm.io module ufedmm.testmodels module ufedmm.ufedmm module UnifiedFreeEnergyDynamics (class in ufedmm.ufedmm)