The mbar
module: MBAR
¶
The mbar
module contains the MBAR
class, which implements the multistate Bennett acceptance ratio (MBAR) method [2].
- class pymbar.MBAR(u_kn, N_k, maximum_iterations=10000, relative_tolerance=1e-07, verbose=False, initial_f_k=None, solver_protocol=None, initialize='zeros', x_kindices=None, n_bootstraps=0, bootstrap_solver_protocol=None, rseed=None)¶
Multistate Bennett acceptance ratio method (MBAR) for the analysis of multiple equilibrium samples.
Notes
Note that this method assumes the data are uncorrelated.
Correlated data must be subsampled to extract uncorrelated (effectively independent) samples.
References
[1] Shirts MR and Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. J. Chem. Phys. 129:124105, 2008 http://dx.doi.org/10.1063/1.2978177
Initialize multistate Bennett acceptance ratio (MBAR) on a set of simulation data.
Upon initialization, the dimensionless free energies for all states are computed. This may take anywhere from seconds to minutes, depending upon the quantity of data. After initialization, the computed free energies may be obtained by a call to
compute_free_energy_differences()
, or expectation at any state of interest can be computed by calls tocompute_expectations()
.- Parameters
u_kn (np.ndarray, float, shape=(K, N_max)) –
u_kn[k,n]
is the reduced potential energy of uncorrelated configuration n evaluated at statek
.u_kln (np.ndarray, float, shape (K, L, N_max)) –
If the simulation is in form
u_kln[k,l,n]
it is converted tou_kn
formatu_kn = [ u_1(x_1) u_1(x_2) u_1(x_3) . . . u_1(x_n) u_2(x_1) u_2(x_2) u_2(x_3) . . . u_2(x_n) . . . u_k(x_1) u_k(x_2) u_k(x_3) . . . u_k(x_n)]
N_k (np.ndarray, int, shape=(K)) –
N_k[k]
is the number of uncorrelated snapshots sampled from statek
. Some may be zero, indicating that there are no samples from that state.We assume that the states are ordered such that the first
N_k
are from the first state, the 2ndN_k
the second state, and so forth. This only becomes important for bar – MBAR does not care which samples are from which state. We should eventually allow this assumption to be overwritten by parameters passed from above, onceu_kln
is phased out.maximum_iterations (int, optional) – Set to limit the maximum number of iterations performed (default 1000)
relative_tolerance (float, optional) – Set to determine the relative tolerance convergence criteria (default 1.0e-6)
verbosity (bool, optional) – Set to True if verbose debug output is desired (default False)
initial_f_k (np.ndarray, float, shape=(K), optional) – Set to the initial dimensionless free energies to use as a guess (default None, which sets all f_k = 0)
solver_protocol (list(dict), string or None, optional, default=None) –
List of dictionaries to define a sequence of solver algorithms and options used to estimate the dimensionless free energies. See pymbar.mbar_solvers.solve_mbar() for details. If None, use the developers best guess at an appropriate algorithm.
if the string is “robust”, it tries “L-BFGS-B” and “adaptive”, with relatively large numbers of iterations.
if “default” or “none”, it will use ‘hybr’ root solver, followed with some rounds of Newton-Raphson if it fails to converge.
The default will try to solve with an adaptive solver algorithm which alternates between self-consistent iteration and Newton-Raphson, where the method with the smallest gradient is chosen to improve numerical stability.
initialize ('zeros' or 'BAR', optional, Default: 'zeros') –
If equal to ‘BAR’, use bar between the pairwise state to initialize the free energies. Eventually, should specify a path; for now, it just does it zipping up the states.
The ‘BAR’ option works best when the states are ordered such that adjacent states maximize the overlap between states. It is up to the user to arrange the states in such an order, or at least close to such an order. If you are uncertain what the order of states should be, or if it does not make sense to think of states as adjacent, then choose ‘zeros’.
x_kindices (np.ndarray, int, shape=(K), default = [0,1,2,3,4...K]) – Describes which state is each sample x is from? Usually doesn’t matter, but it does for bar. As a default, we assume the samples are in
K
order (the firstN_k[0]
samples are from the 0th state, the nextN_k[1]
samples from the 1st state, and so forth.n_bootstraps (int) – How many bootstrap free energies will be computed? If None, no bootstraps will be computed. computing uncertainties with bootstraps is only possible if this is > 0. (default: None)
bootstrap_solver_protocol (list(dict), string or None, optional, default=None) – We usually just do steps of adaptive sampling without. “robust” would be the backup. Default: dict(method=”adaptive”, options=dict(min_sc_iter=0)),
Notes
The reduced potential energy
u_kn[k,n] = u_k(x_{ln})
, where the reduced potential energyu_l(x)
is defined (as in the text) by:u_k(x) = beta_k [ U_k(x) + p_k V(x) + mu_k' n(x) ]
wherebeta_k = 1/(k_B T_k)
is the inverse temperature of conditionk
, where k_B is Boltzmann’s constantU_k(x)
is the potential energy function for statek
p_k
is the pressure at statek
(if an isobaric ensemble is specified)V(x)
is the volume of configurationx
mu_k
is the M-vector of chemical potentials for the various species, if a (semi)grand ensemble is specified, and'
denotes transposen(x)
is the M-vector of numbers of the various molecular species for configurationx
, corresponding to the chemical potential components ofmu_m
.x_n
indicates that the samples are fromk
different simulations of then
states. These simulations need only be a subset of the k states.The configurations
x_ln
must be uncorrelated. This can be ensured by subsampling a correlated timeseries with a period larger than the statistical inefficiency, which can be estimated from the potential energy timeseries{u_k(x_ln)}_{n=1}^{N_k}
using the provided utilitypymbar.timeseries.statistical_inefficiency()
. See the help for this function for more information.Examples
>>> from pymbar import testsystems >>> (x_n, u_kn, N_k, s_n) = testsystems.HarmonicOscillatorsTestCase().sample(mode='u_kn') >>> mbar = MBAR(u_kn, N_k)
- property W_nk¶
Retrieve the weight matrix W_nk from the MBAR algorithm.
Necessary because they are stored internally as log weights.
- Returns
weights – NxK matrix of weights in the MBAR covariance and averaging formulas
- Return type
np.ndarray, float, shape=(N, K)
- compute_covariance_of_sums(d_ij, K, a)¶
We wish to calculate the variance of a weighted sum of free energy differences. for example
var(\sum a_i df_i)
.We explicitly lay out the calculations for four variables (where each variable is a logarithm of a partition function), then generalize.
The uncertainty in the sum of two weighted differences is
var(a1(f_i1 - f_j1) + a2(f_i2 - f_j2)) = a1^2 var(f_i1 - f_j1) + a2^2 var(f_i2 - f_j2) + 2 a1 a2 cov(f_i1 - f_j1, f_i2 - f_j2) cov(f_i1 - f_j1, f_i2 - f_j2) = cov(f_i1,f_i2) - cov(f_i1,f_j2) - cov(f_j1,f_i2) + cov(f_j1,f_j2)
call:
f_i1 = a f_j1 = b f_i2 = c f_j2 = d a1^2 var(a-b) + a2^2 var(c-d) + 2a1a2 cov(a-b,c-d)
we want
2cov(a-b,c-d) = 2cov(a,c)-2cov(a,d)-2cov(b,c)+2cov(b,d)
, sincevar(x-y) = var(x) + var(y) - 2cov(x,y)
, then,2cov(x,y) = -var(x-y) + var(x) + var(y)
. So, we get2cov(a,c) = -var(a-c) + var(a) + var(c) -2cov(a,d) = +var(a-d) - var(a) - var(d) -2cov(b,c) = +var(b-c) - var(b) - var(c) 2cov(b,d) = -var(b-d) + var(b) + var(d)
adding up, finally :
2cov(a-b,c-d) = 2cov(a,c)-2cov(a,d)-2cov(b,c)+2cov(b,d) = - var(a-c) + var(a-d) + var(b-c) - var(b-d) a1^2 var(a-b)+a2^2 var(c-d)+2a1a2cov(a-b,c-d) = a1^2 var(a-b)+a2^2 var(c-d)+a1a2 [-var(a-c)+var(a-d)+var(b-c)-var(b-d)] var(a1(f_i1 - f_j1) + a2(f_i2 - f_j2)) = a1^2 var(f_i1 - f_j1) + a2^2 var(f_i2 - f_j2) + 2a1 a2 cov(f_i1 - f_j1, f_i2 - f_j2) = a1^2 var(f_i1 - f_j1) + a2^2 var(f_i2 - f_j2) + a1 a2 [-var(f_i1 - f_i2) + var(f_i1 - f_j2) + var(f_j1-f_i2) - var(f_j1 - f_j2)]
assume two arrays of free energy differences, and and array of constant vectors a. we want the variance
var(\sum_k a_k (f_i,k - f_j,k))
Each set is separated from the other by an offset K same process applies with the sum, with the single var terms and the pair terms- Parameters
d_ij (a matrix of standard deviations of the quantities f_i - f_j) –
K (The number of states in each 'chunk', has to be constant) –
outputs (KxK variance matrix for the sums or differences
\sum a_i df_i
) –
- compute_effective_sample_number(verbose=False)¶
Compute the effective sample number of each state; essentially, an estimate of how many samples are contributing to the average at given state. See pymbar/examples for a demonstration.
It also counts the efficiency of the sampling, which is simply the ratio of the effective number of samples at a given state to the total number of samples collected. This is printed in verbose output, but is not returned for now.
- Returns
N_eff – estimated number of samples contributing to estimates at each state i. An estimate to how many samples collected just at state i would result in similar statistical efficiency as the MBAR simulation. Valid for both sampled states (in which the weight will be greater than N_k[i], and unsampled states.
- Return type
np.ndarray, float, shape=(K)
- Parameters
verbose (print out information about the effective number of samples) –
Notes
Using Kish (1965) formula (Kish, Leslie (1965). Survey Sampling. New York: Wiley)
As the weights become more concentrated in fewer observations, the effective sample size shrinks. from http://healthcare-economist.com/2013/08/22/effective-sample-size/
effective number of samples contributing to averages carried out at state i = (\sum_{n=1}^N w_in)^2 / \sum_{n=1}^N w_in^2 = (\sum_{n=1}^N w_in^2)^-1
the effective sample number is most useful to diagnose when there are only a few samples contributing to the averages.
Examples
>>> from pymbar import testsystems >>> [x_kn, u_kln, N_k, s_n] = testsystems.HarmonicOscillatorsTestCase().sample() >>> mbar = MBAR(u_kln, N_k) >>> N_eff = mbar.compute_effective_sample_number()
- compute_entropy_and_enthalpy(u_kn=None, uncertainty_method=None, verbose=False, warning_cutoff=1e-10)¶
Decompose free energy differences into enthalpy and entropy differences.
Compute the decomposition of the free energy difference between states 1 and N into reduced free energy differences, reduced potential (enthalpy) differences, and reduced entropy (S/k) differences.
- Parameters
u_kn (float, NxK array) – The energies of the state that are being used.
uncertainty_method (str , optional) – Choice of method used to compute asymptotic covariance method, or None to use default See help for computeAsymptoticCovarianceMatrix() for more information on various methods. if method = “bootstrap” then uncertainty over bootstrap samples is used. with bootstraps. (default: None)
warning_cutoff (float, optional) – Warn if squared-uncertainty is negative and larger in magnitude than this number (default: 1.0e-10)
- Returns
Results dictionary with the following keys
’Delta_f’ (np.ndarray, float, shape=(K, K)) – results[‘Delta_f’] is the dimensionless free energy difference f_j - f_i
’dDelta_f’ (np.ndarray, float, shape=(K, K)) – uncertainty in results[‘Delta_f’]
’Delta_u’ (np.ndarray, float, shape=(K, K)) – results[‘Delta_u’] is the reduced potential energy difference u_j - u_i
’dDelta_u’ (np.ndarray, float, shape=(K, K)) – uncertainty in results[‘Delta_u’]
’Delta_s’ (np.ndarray, float, shape=(K, K)) – results[‘Delta_s’] is the reduced entropy difference S/k between states i and j (s_j - s_i)
’dDelta_s’ (np.ndarray, float, shape=(K, K)) – uncertainty in results[‘Delta_s’]
Examples
>>> from pymbar import testsystems >>> x_n, u_kn, N_k, s_n = testsystems.HarmonicOscillatorsTestCase().sample(mode='u_kn') >>> mbar = MBAR(u_kn, N_k) >>> results = mbar.compute_entropy_and_enthalpy()
- compute_expectations(A_n, u_kn=None, output='averages', state_dependent=False, compute_uncertainty=True, uncertainty_method=None, warning_cutoff=1e-10, return_theta=False)¶
Compute the expectation of an observable of a phase space function.
Compute the expectation of an observable of a single phase space function A(x) at all states where potentials are generated.
- Parameters
A_n (np.ndarray, float) – A_n (N_max np float64 array) - A_n[n] = A(x_n)
u_kn (np.ndarray) – u_kn (energies of state of interest length N) default is self.u_kn
output (string, optional) – ‘averages’ outputs expectations of observables and ‘differences’ outputs a matrix of differences in the observables.
compute_uncertainty (bool, optional) – If False, the uncertainties will not be computed (default : True)
uncertainty_method (string, optional) – Choice of method used to compute asymptotic covariance method, or None to use default See help for _computeAsymptoticCovarianceMatrix() for more information on various methods. if uncertainty_method = “bootstrap”, then uncertainty over bootstrap samples is used. (default: None)
warning_cutoff (float, optional) – Warn if squared-uncertainty is negative and larger in magnitude than this number (default: 1.0e-10)
state_dependent (bool, whether the expectations are state-dependent.) –
- Returns
Results dictionary with the following keys
’mu’ (np.ndarray, float) – if output is ‘averages’ A_i (K np float64 array) - A_i[i] is the estimate for the expectation of A(x) for state i. if output is ‘differences’
’sigma’ (np.ndarray, float) – dA_i (K np float64 array) - dA_i[i] is uncertainty estimate (one standard deviation) for A_i[i] or dA_ij (K np float64 array) - dA_ij[i,j] is uncertainty estimate (one standard deviation) for the difference in A beteen i and j or None, if compute_uncertainty is False.
’Theta’ (((KxK np float64 array): Covariance matrix of log weights)
References
See Section IV of [1].
Examples
>>> from pymbar import testsystems >>> (x_n, u_kn, N_k, s_n) = testsystems.HarmonicOscillatorsTestCase().sample(mode='u_kn') >>> mbar = MBAR(u_kn, N_k) >>> A_n = x_n >>> results = mbar.compute_expectations(A_n) >>> A_n = u_kn[0,:] >>> results = mbar.compute_expectations(A_n, output='differences')
- compute_expectations_inner(A_n, u_ln, state_map, uncertainty_method=None, warning_cutoff=1e-10, return_theta=False)¶
Compute the expectations of multiple observables of phase space functions in multiple states.
Compute the expectations of multiple observables of phase space functions [A_0(x),A_1(x),…,A_i(x)] along with the covariances of their estimates at multiple states.
Intended as an internal function to keep all the optimized and robust expectation code in one place, but will leave it open to allow for later modifications and uses.
It calculates all input observables at all states which are specified by the list of states in the state list.
- Parameters
A_n (np.ndarray, float, shape=(I, N)) – A_in[i,n] = A_i(x_n), the value of phase observable i for configuration n
u_ln (np.ndarray, float, shape=(L, N)) – u_ln[l,n] is the reduced potential of configuration n at state l if u_ln = None, we use self.u_kn
state_map (np.ndarray, int, shape (2,NS) or shape(1,NS)) – If state_map has only one dimension where NS is the total number of states we want to simulate things a. The list will be of the form
[[0,1,2],[0,1,1]]
. This particular example indicates we want to output the properties of three observables total: the first property A[0] at the 0th state, the 2nd property A[1] at the 1th state, and the 2nd property A[1] at the 2nd state. This allows us to tailor our output to a large number of different situations.uncertainty_method (string, optional) – Choice of method used to compute asymptotic covariance method, or None to use default See help for _computeAsymptoticCovarianceMatrix() for more information on various methods. The exception is the “bootstrap” option, which required n_boostraps being defined at initialization of MBAR. (default: None)
warning_cutoff (float, optional) – Warn if squared-uncertainty is negative and larger in magnitude than this number (default: 1.0e-10)
return_theta (bool, optional) – Whether or not to return the theta matrix. Can be useful for complicated differences of observables.
- Returns
result_vals (dictionary)
Keys in the result_vals dictionary
’observables’ (np.ndarray, float, shape = (S)) – results_vals[‘observables’][i] is the estimate for the expectation of A_state_map[i](x) at the state specified by u_n[state_map[i],:]
’Theta’ (np.ndarray, float, shape = (K+len(state_list), K+len(state_list)) the covariance matrix of log weights.)
’Amin’ (np.ndarray, float, shape = (S), needed for reconstructing the covariance one level up.)
’f’ (np.ndarray, float, shape = (K+len(state_list)), ‘free energies’ of the new states (i.e. ln (<A>-Amin+logfactor)) as the log form is easier to work with.)
’bootstrapped_observables’ (np.ndarray, float, shape = (n_boostraps,S), array of the observables bootstrapped over random samples.)
’bootstrapped_f’ (np.ndarray, float, shape = (n_boostraps,S), free energies ‘f’ bootstrapped over random samples.)
Notes
Situations this will be used for:
Multiple observables, single state (called though compute_multiple_expectations)
Single observable, multiple states (called through compute_expectations)
This has two cases : observables that don’t change with state, and observables that do change with state. For example, the set of energies at state k consist in energy function of state 1 evaluated at state 1, energies of state 2 evaluated at state 2, and so forth.
Computing only free energies at new states.
Examples
>>> from pymbar import testsystems >>> (x_n, u_kn, N_k, s_n) = testsystems.HarmonicOscillatorsTestCase().sample(mode='u_kn') >>> mbar = MBAR(u_kn, N_k) >>> A_n = np.array([x_n,x_n**2,x_n**3]) >>> u_n = u_kn[:2,:] >>> state_map = np.array([[0,0],[1,0],[2,0],[2,1]],int) >>> results = mbar.compute_expectations_inner(A_n, u_n, state_map)
- compute_free_energy_differences(compute_uncertainty=True, uncertainty_method=None, warning_cutoff=1e-10, return_theta=False)¶
Compute and return the dimensionless free energy differences and uncertainties among all thermodynamic states.
- Parameters
compute_uncertainty (bool, optional) – If False, the uncertainties will not be computed (default : True)
uncertainty_method (string, optional) – Choice of method used to compute asymptotic covariance method, or None to use default. See help for _computeAsymptoticCovarianceMatrix() for more information on various methods. (default : svd) The exception is the “bootstrap” option, which requires n_boostraps being defined upon initialization of MBAR.
warning_cutoff (float, optional) – Warn if squared-uncertainty is negative and larger in magnitude than this number (default : 1.0e-10)
return_theta (bool, optional) – Whether or not to return the theta matrix. Can be useful for complicated differences.
- Returns
Results dictionary with the following keys
’Delta_f’ (np.ndarray, float, shape=(K, K)) – Deltaf_ij[i,j] is the estimated free energy difference
’dDelta_f’ (np.ndarray, float, shape=(K, K)) – If compute_uncertainty==True, dDeltaf_ij[i,j] is the estimated statistical uncertainty (one standard deviation) in Deltaf_ij[i,j]. Otherwise not included.
’Theta’ (np.ndarray, float, shape=(K, K)) – The theta_matrix if return_theta==True, otherwise not included.
Notes
Computation of the covariance matrix may take some time for large K.
The reported statistical uncertainty should, in the asymptotic limit, reflect one standard deviation for the normal distribution of the estimate. The true free energy difference should fall within the interval [-df, +df] centered on the estimate 68% of the time, and within the interval [-2 df, +2 df] centered on the estimate 95% of the time. This will break down in cases where the number of samples is not large enough to reach the asymptotic normal limit.
See Section III of Reference [1].
Examples
>>> from pymbar import testsystems >>> (x_n, u_kn, N_k, s_n) = testsystems.HarmonicOscillatorsTestCase().sample(mode='u_kn') >>> mbar = MBAR(u_kn, N_k) >>> results = mbar.compute_free_energy_differences()
- compute_multiple_expectations(A_in, u_n, compute_uncertainty=True, compute_covariance=False, uncertainty_method=None, warning_cutoff=1e-10, return_theta=False)¶
Compute the expectations of multiple observables of phase space functions.
Compute the expectations of multiple observables of phase space functions [A_0(x),A_1(x),…,A_i(x)] at a single state, along with the error in the estimates and the uncertainty in the estimates. The state is specified by the choice of u_n, which is the energy of the n samples evaluated at a the chosen state.
- Parameters
A_in (np.ndarray, float, shape=(I, k, N)) – A_in[i,n] = A_i(x_n), the value of phase observable i for configuration n at state of interest
u_n (np.ndarray, float, shape=(N)) – u_n[n] is the reduced potential of configuration n at the state of interest
compute_uncertainty (bool, optional, default=True) – If True, calculate the uncertainty
compute_covariance (bool, optional, default=False) – If True, calculate the covariance
uncertainty_method (string, optional) – Choice of method used to compute asymptotic covariance method, or None to use default See help for computeAsymptoticCovarianceMatrix() for more information on various methods. if method = “bootstrap” then uncertainty over bootstrap samples is used. with bootstraps. (default: None)
warning_cutoff (float, optional) – Warn if squared-uncertainty is negative and larger in magnitude than this number (default : 1.0e-10)
- Returns
Results dictionary with the following keys
’mu’ (np.ndarray, float, shape=(I)) – result_vals[‘mu’] is the estimate for the expectation of A_i(x) at the state specified by u_kn
’sigma’ (np.ndarray, float, shape = (I)) – result_vals[‘sigma’] is the uncertainty in the expectation of A_state_map[i](x) at the state specified by u_n[state_map[i],:] or None if compute_uncertainty is False
’covariances’ (np.ndarray, float, shape=(I, I)) – result_vals[‘covariances’] is the COVARIANCE in the estimates of A_i[i] and A_i[j]: we can’t actually take a square root or None if compute_covariance is False
’Theta’ (np.ndarray, float, shape=(I, I), covariances of the log weights, useful for some additional calculations.)
Examples
>>> from pymbar import testsystems >>> (x_n, u_kn, N_k, s_n) = testsystems.HarmonicOscillatorsTestCase().sample(mode='u_kn') >>> mbar = MBAR(u_kn, N_k) >>> A_in = np.array([x_n,x_n**2,x_n**3]) >>> u_n = u_kn[0,:] >>> results = mbar.compute_multiple_expectations(A_in, u_kn)
- compute_overlap()¶
Compute estimate of overlap matrix between the states.
- Parameters
None –
- Returns
Results dictionary with the following keys
’scalar’ (np.ndarray, float, shape=(K, K)) – One minus the largest nontrival eigenvalue (largest is 1 or -1)
’eigenvalues’ (np.ndarray, float, shape=(K)) – The sorted (descending) eigenvalues of the overlap matrix.
’matrix’ (np.ndarray, float, shape=(K, K)) – Estimated state overlap matrix : O[i,j] is an estimate of the probability of observing a sample from state i in state j
Notes
W.T * W \approx \int (p_i p_j /\sum_k N_k p_k)^2 \sum_k N_k p_k dq^N = \int (p_i p_j /\sum_k N_k p_k) dq^N
Multiplying elementwise by N_i, the elements of row i give the probability for a sample from state i being observed in state j.
Examples
>>> from pymbar import testsystems >>> (x_kn, u_kn, N_k, s_n) = testsystems.HarmonicOscillatorsTestCase().sample(mode='u_kn') >>> mbar = MBAR(u_kn, N_k) >>> results = mbar.compute_overlap()
- compute_perturbed_free_energies(u_ln, compute_uncertainty=True, uncertainty_method=None, warning_cutoff=1e-10)¶
Compute the free energies for a new set of states.
Here, we desire the free energy differences among a set of new states, as well as the uncertainty estimates in these differences.
- Parameters
u_ln (np.ndarray, float, shape=(L, Nmax)) – u_ln[l,n] is the reduced potential energy of uncorrelated configuration n evaluated at new state k. Can be completely indepednent of the original number of states.
compute_uncertainty (bool, optional, default=True) – If False, the uncertainties will not be computed (default: True)
uncertainty_method (string, optional) – Choice of method used to compute asymptotic covariance method, or None to use default See help for computeAsymptoticCovarianceMatrix() for more information on various methods. if method = “bootstrap” then uncertainty over bootstrap samples is used. with bootstraps. (default: None)
warning_cutoff (float, optional) – Warn if squared-uncertainty is negative and larger in magnitude than this number (default: 1.0e-10)
- Returns
Results dictionary with the following entries.
’Delta_f’ (np.ndarray, float, shape=(L, L)) – result_vals[‘Delta_f’] = f_j - f_i, the dimensionless free energy difference between new states i and j
’dDelta_f’ (np.ndarray, float, shape=(L, L)) – result_vals[‘dDelta_f’] is the estimated statistical uncertainty in result_vals[‘Delta_f’] or not included if compute_uncertainty is False
Examples
>>> from pymbar import testsystems >>> (x_n, u_kn, N_k, s_n) = testsystems.HarmonicOscillatorsTestCase().sample(mode='u_kn') >>> mbar = MBAR(u_kn, N_k) >>> results = mbar.compute_perturbed_free_energies(u_kn)
- weights()¶
Retrieve the weight matrix W_nk from the MBAR algorithm.
Necessary because they are stored internally as log weights.
- Returns
weights – NxK matrix of weights in the MBAR covariance and averaging formulas
- Return type
np.ndarray, float, shape=(N, K)