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Table of Contents

  • Installation Guide
    • Dependencies
    • Download and install ThermoLIB
      • Direct install using pip
      • Source code download and install
    • Update ThermoLIB
    • Test installation
  • User Guide
    • Constructing 1D histograms & free energy profiles
      • Construct a 1D histrogam …
        • … from a single simulation
        • … from multiple simulations using WHAM
      • Constructing a 1D free energy profile …
        • … using the constructor
        • … reading from a text file
        • … from a histogram
    • Constructing 2D histograms & free energy surfaces
      • Constructing a 2D histogram …
        • … from single simulation
        • … from multiple simulations using WHAM
      • Constructing a 2D free energy surface …
        • … using the constructor
        • … reading from a text file
        • … from a histogram
    • Computing the correlation time
      • Fit to autocorrelation function for single trajectory
      • Compute correlation time for trajectory series
    • Error estimation
      • Without correlations
      • With correlations
    • Plotting histograms and FEP/FES
      • 1D Histograms & free energy profile
      • 2D Histograms & free energy surfaces
    • Extracting micro- and macrostate free energy
    • Computing the reaction rate
    • Transformations of the FEP/FES
      • Deterministic transformation
        • 1 dimensional
        • 2 dimensional
      • Probabilistic transformation
    • (De)projections of the FEP/FES
      • Projecting 2D FES to 1D FEP
      • Deprojecting 1D FEP to 2D FES
  • Tutorials
    • Tutorial 1 - Construction of 1D free energy profile using WHAM
      • Introduction
      • WHAM without error estimation
      • WHAM with error estimation
      • Defining macrostates and microstates
    • Tutorial 2 - Extracting kinetic reaction rates in 1D
      • Introduction
      • Construct free energy profile
      • Compute rate prefactor
      • Add kinetic information to FEP plot
    • Tutorial 3 - Construction of 2D free energy surface using WHAM
      • Introduction
      • 2D WHAM without error estimation
      • 2D WHAM with error estimate
      • Alternative plotting
    • Tutorial 4 - Advanced techniques in error estimation
      • Introduction
      • Impact correlation between samples on FEP
      • Estimating the autocorrelation time
      • Constructing the FEP with correlated error estimate
      • Evaluating the correlated error estimate
        • Delayed-strided WHAM profiles
        • Blocked WHAM profile
        • Bootstrapped WHAM profiles
      • Covariance between different points on FEP
      • Error propagation
    • Tutorial 5 - Projection of 2D FES to 1D FEP with error propagation
      • Introduction
      • Constructing 2D FES
      • Projection onto 1D profile
        • Along predefined direction
        • Along any custom direction
      • Error propagation
        • Deal with the unsufficiently sampled edges of phase space in FES projection
    • Tutorial 6 - Deprojection to extract energetic contribution to free energy
      • Introduction
      • Construct 1D FEP
      • Deproject to 2D FES
        • Direct route - 2D WHAM
        • Indirect route - deproject 1D FEP
        • CONSISTENCY CHECK: project 2D FES to 1D FEP
      • U(CV) profile
        • Method 1 - from 2D FES
        • Method 2 - from conditional probability
        • comparison
    • Tutorial 7 - Transformations of 1D FEP and kinetics
      • Introduction
      • FEP and rate with original CV
      • FEP and rate in terms of alternative CV
    • Tutorial 8 - Transformation of 2D free energy surfaces
      • Introduction
      • Construction of original 2D FES
      • Transformation to new CVs
      • Projection comparison
  • Reference Guide
    • Thermodynamics – thermolib.thermodynamics
      • Free energy profiles – thermolib.thermodynamics.fep
        • BaseFreeEnergyProfile
        • BaseProfile
        • FreeEnergySurface2D
        • SimpleFreeEnergyProfile
        • plot_profiles()
      • Histograms – thermolib.thermodynamics.histogram
        • Histogram1D
        • Histogram2D
        • plot_histograms()
      • Trajectory readers – thermolib.thermodynamics.trajectory
        • ASEExtendedXYZReader
        • CVComputer
        • ColVarReader
        • HDF5Reader
      • Bias potentials – thermolib.thermodynamics.bias
        • BiasPotential1D
        • BiasPotential2D
        • MultipleBiasses1D
        • Parabola1D
        • Parabola2D
        • PlumedSplinePotential1D
        • Polynomial1D
      • Collective variables – thermolib.thermodynamics.cv
        • Average
        • CenterOfMass
        • CenterOfPosition
        • CoordinationNumber
        • Difference
        • DistOrthProjOrig
        • Distance
        • DistanceCOP
        • DotProduct
        • LinearCombination
        • Minimum
        • NormalToPlane
        • NormalizedAxis
        • OrthogonalDistanceToPore
      • State – thermolib.thermodynamics.state
        • Integrate
        • Maximum
        • Minimum
      • Conditional probability – thermolib.thermodynamics.condprob
        • ConditionalProbability1D1D
        • ConditionalProbability1D2D
    • Kinetics – thermolib.kinetics
      • Rate constant – thermolib.kinetics.rate
        • BaseRateFactor
        • RateFactorEquilibrium
    • Error distributions – thermolib.error
      • ErrorArray
        • ErrorArray.mean()
        • ErrorArray.nsigma_conf_int()
        • ErrorArray.sample()
        • ErrorArray.std()
      • GaussianDistribution
        • GaussianDistribution.copy()
        • GaussianDistribution.from_samples()
        • GaussianDistribution.log_from_loggaussian()
        • GaussianDistribution.mean()
        • GaussianDistribution.nsigma_conf_int()
        • GaussianDistribution.print()
        • GaussianDistribution.sample()
        • GaussianDistribution.set_ref()
        • GaussianDistribution.shift()
        • GaussianDistribution.std()
      • LogGaussianDistribution
        • LogGaussianDistribution.copy()
        • LogGaussianDistribution.exp_from_gaussian()
        • LogGaussianDistribution.from_samples()
        • LogGaussianDistribution.mean()
        • LogGaussianDistribution.nsigma_conf_int()
        • LogGaussianDistribution.sample()
        • LogGaussianDistribution.set_ref()
        • LogGaussianDistribution.shift()
        • LogGaussianDistribution.std()
      • MultiDistribution
        • MultiDistribution.corr()
      • MultiGaussianDistribution
        • MultiGaussianDistribution.copy()
        • MultiGaussianDistribution.cov()
        • MultiGaussianDistribution.from_samples()
        • MultiGaussianDistribution.log_from_loggaussian()
        • MultiGaussianDistribution.mean()
        • MultiGaussianDistribution.nsigma_conf_int()
        • MultiGaussianDistribution.plot_corr_matrix()
        • MultiGaussianDistribution.sample()
        • MultiGaussianDistribution.set_ref()
        • MultiGaussianDistribution.std()
      • MultiLogGaussianDistribution
        • MultiLogGaussianDistribution.copy()
        • MultiLogGaussianDistribution.cov()
        • MultiLogGaussianDistribution.exp_from_gaussian()
        • MultiLogGaussianDistribution.from_samples()
        • MultiLogGaussianDistribution.mean()
        • MultiLogGaussianDistribution.nsigma_conf_int()
        • MultiLogGaussianDistribution.plot_corr_matrix()
        • MultiLogGaussianDistribution.sample()
        • MultiLogGaussianDistribution.std()
      • Propagator
        • Propagator.calc_fun_values()
        • Propagator.gen_args_samples()
        • Propagator.get_distribution()
        • Propagator.reset()
      • SampleDistribution
        • SampleDistribution.from_samples()
        • SampleDistribution.mean()
        • SampleDistribution.sample()
        • SampleDistribution.set_ref()
        • SampleDistribution.shift()
        • SampleDistribution.std()
    • Tools – thermolib.tools
      • blav()
      • corrtime_from_acf()
      • decorrelate()
      • extract_polynomial_bias_info()
      • fisher_matrix_mle_probdens()
      • format_scientific()
      • h5_read_dataset()
      • integrate()
      • integrate2d()
      • interpolate_surface_2d()
      • invert_fisher_to_covariance()
      • multivariate_normal()
      • plot_histograms_1d()
      • plot_histograms_overlap_1d()
      • read_wham_input()
      • rolling_average()
    • Extensions – thermolib.ext
      • wham1d_bias()
      • wham1d_error()
      • wham1d_hs()
      • wham1d_scf()
      • wham2d_bias()
      • wham2d_error()
      • wham2d_hs()
      • wham2d_scf()
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