UWHAM (version 1.0)

uwham: Unbinned weighted histogram analysis method (UWHAM) for estimating free energies

Description

This function implements UWHAM for estimating log-normalizing constants (or free energies) and expectations from multiple distributions (such as multiple generalized ensembles) as described in Tan et al. (2012).

Usage

uwham(label=NULL, logQ, size=NULL, base = NULL, init = NULL, 
      fisher = TRUE)

Arguments

label

A vector of length N of labels between 1 to M such that label[i]=j when ith observation is obtained from jth thermodynamic state; either label or size must be provided; if fisher=FALSE and if label=NULL, then label is set such that the first size[1] observations are assumed to be from state 1, the next size[2] observations from state 2, etc.

logQ

N x M matrix of log unnormalized densities (such as \(1/kT\) times negative potential energies), where N is the total sample size, i.e., sum(size), and M is the number of thermodynamic states for which free energies are to be computed; the ith row of logQ correspond to ith observations and the jth column correspond to jth thermodynamic state.

size

A vector of length M, giving the individual sample sizes for the M thermodynamic states, ordered as the columns of logQ; if NULL, then label is required and used to compute size.

base

The baseline index, between 1 to M, for the thermodynamic state (with sample size >0) whose free energy is set to 0; if NULL, then base is set to the first index j such that size[j]>0.

init

A vector of length M, giving the initial values of the log-normalizing constants (or log of the partition functions); if NULL, then init is set to the zero vector.

fisher

Logical; if NULL, no variance estimation; if TRUE, variance estimation is based on Fisher information; if FALSE, variance estimation is based on the Sandwich variance formula (see the details).

Value

ze

The vector of estimated log-normalizing constants (or log of the partition functions).

ve

The vector of estimated variances for ze, if fisher!=NULL.

Ve

The estimated variance-covariance matrix for ze, if fisher!=NULL.

W

The N x M matrix of UWHAM weights for each of the N observations at each of the M thermodynamic states.

check

The column averages of W[,sampled]; the elements of check should be equal to 1 to indicate a valid convergence of trust.

out

The output of trust used to minimize the objective function; see help(trust).

label

Same as argument label.

size

Same as argument size.

base

Same as argument base.

Details

The UWHAM method results from a number of interesting, sometimes independent, developments in physics and statistics. See Kong et al. (2003) for a formal statistical treatment along with earlier references, and Tan et al. (2012) for a more accessible account, presenting the method as a binless extension of the Weighted Histogram Analysis Method (WHAM) widely known in physics and chemistry (e.g., Ferrenberg and Swendsen 1989). The possibility of obtaining free energies from a binless extension of WHAM was noticed by various authors (e.g., Kumar et al. 1992; Newman & Barkema 1999). The binless method was later reintroduced by Shirts & Chodera (2008) to the physics literature and was called the Multi-state Bennet Acceptance Ratio method (MBAR) because it can be interpreted as a multi-state extension of the Bennet Acceptance Ratio (BAR) method. An implementation of MBAR in the Python language developed by Shirts & Chodera is freely available (see https://simtk.org/home/pymbar). The UWHAM package, while adopting an alternative numerical approach, provides identical point estimates compared to the MBAR Python package. In addition, the UWHAM package provides variance estimation based on variance formulas without using generalized inverses or, for correlated data, by block bootstrap.

A typical application of UWHAM involves the computation of the relative free energies of a series of thermodynamic states differing in environmental conditions (temperature for example) and/or Hamiltonian parameters (such as the strength of biasing potentials) from data collected at these thermodynamic states. The method takes as input the reduced energies (such as the inverse temperature times the negative of the potential energy for canonical ensembles differing in temperature) of the observations at all thermodynamic states of interest. In addition to the free energies, the output includes estimates of the thermodynamic weights of the observations for all states to be used for thermodynamic reweighting calculations.

The UWHAM method is statistically optimal in yielding the smallest asymptotic variances, provided that the individual samples are independent and the observations in each sample are also independent (Tan 2004).

To compute point estimates, the method is implemented here by minimizing a convex objective function, as described in Tan et al. (2012). This approach can be more effective than solving the nonlinear equations by the self-consistency or the Newton-Raphson algorithm. Currently, the optimization is done by using the R package trust.

Variance estimation provided here is based on the Fisher information or the Sandwich variance formula, as presented in Tan et al. (2012). In contrast with the Sandwich formula, the Fisher information based formula does not require labels indicating which thermodynamic state each observation is obtained from (see the dataset ligand2.hard). The analytical variance formulas are consistent when the observations are considered independent. Alternatively, variance estimation can be done by block bootstrap, implemented in uwham.boot.

References

Ferrenberg, A.M. and Swendsen, R.H. (1989) "Optimized Monte Carlo data analysis," Physics Review Letters, 63, 1195-1198.

Kong, A., McCullagh, P., Meng, X.-L., Nicolae, D., and Tan, Z. (2003) "A theory of statistical models for Monte Carlo integration" (with discussion), Journal of the Royal Statistical Society, Ser. B, 65, 585-618.

Kumar, S., Bouzida, D., Swendsen, R.H., Kollman, P.A. and Rosenberg, J.M. (1992) "The Weighted Histogram Analysis Method for free-energy calculations on biomolecules. I. The method," Journal of Computational Chemistry, 13, 1011-1021.

Newman, M.E.J. and Barkema, G.T. (1999) Monte Carlo Methods in Statistical Physics, Oxford University Press, New York.

Shirts, M.R. and J. D. Chodera, J.D. (2008) "Statistically optimal analysis of samples from multiple equilibrium states," Journal of Chemical Physics, 129, 124105.

Tan, Z. (2004) "On a likelihood approach for Monte Carlo integration," Journal of the American Statistical Association, 99, 1027-1036.

Tan, Z., Gallicchio, E., Lapelosa, M., and Levy, R.M. (2012) "Theory of binless multi-state free energy estimation with applications to protein-ligand binding," Journal of Chemical Physics, 136, 144102.

Examples

# NOT RUN {
#######################################
############## example 1 ##############  
#######################################

# This example illustrates the calculation of the standard free energy
# of binding of a ligand to a protein receptor by means of an alchemical
# perturbation potential of the form lambda*binding_energy(r), where
# lambda is a scaling parameter (lambda=0 corresponds to the
# protein-ligand uncoupled state, and lambda=1 corresponds to the
# coupled state) and binding_energy(r) is the (solvent averaged)
# potential energy of conformation r of the complex relative to one in
# which the receptor and the ligand are rigidly displaced at infinite
# separation. See Gallicchio et al., J. Chem. Theory Comput. 6,
# 2961-2977 (2010), and Tan et al. J. Chem. Phys., 136, 144102 (2012).

# Inverse temperature beta, in kcal/mol^-1
bet <- 1.0/(0.001986209*300.0)

# negative reduced potential function -beta*lambda*binding_energy.
#  "x" is the binding energy of a structure of the complex and "lam" the
#  value of lambda at which to compute the reduced energy
npot.fcn <- function(x, lam)
   -bet*lam*x

# values of lambda for the calculation with a "hard-core" potential 
lam <- c(0.0, 0.000000001, 0.00000001, 0.0000001, 0.000001, 0.00001, 0.0001,
         0.001, 0.01, 0.1, 0.15, 0.25, 0.35, 0.5, 0.6, 0.75, 0.9, 1.0)

#number of alchemical states
m <- length(lam)

# load binding energies
data(ligand2.hard)
lig.data <- ligand2.hard$V1

# 1000 observations at each lambda state
size <- rep(1000, m)

# total sample size
N <- sum(size)

# compute negative potential of each observation at each lambda state
neg.pot <- matrix(0, N,m)
for (j in 1:length(lam))
  neg.pot[,j] <- npot.fcn(x=lig.data, lam=lam[j])

# estimate free energies using UWHAM
out <- uwham(logQ=neg.pot, size=size, fisher=TRUE)

# convergence diagnosis: the elements should be equal to 1 
out$check

# the "ze" values are dimensionless free energies, that is the
# log of the partition functions (log Z). 
# To obtain thermodynamic free energies, multiply by -kT.
# 0.71 kcal/mol is the standard state correction; see
# Lapelosa et al. J Chem Theory Comput, 8, 44-60 (2012).
-out$ze/bet + 0.71

# variances of free energies from Fisher information
sqrt(out$ve)/bet

# perform block bootstrap for free energies to take into account
# time correlations in the binding energy data
# To save time for package checking, this is not run.
#out.boot <- uwham.boot(proc.type="parallel", block.size=50, boot.size=100, 
#                       logQ=neg.pot, size=size)
#
#-out.boot$ze/bet + 0.71
#sqrt(out.boot$ve)/bet

# estimation of average binding energies and variances 
# at lambda = 0.6, 0.75, 0.9, 1.0
state <- 15:18
out.phi <- uwham.phi(phi=lig.data, state=state, out.uwham=out, fisher=TRUE)

out.phi$phi
out.phi$phi.v 

# block bootstrap for both free energies and expectations
# To save time for package checking, this is not run.
#out.boot <- uwham.boot(proc.type="parallel", block.size=50, boot.size=100, 
#                       logQ=neg.pot, size=size, 
#                       phi=lig.data, state=state)
#
#out.boot$phi
#out.boot$phi.v

################################################
## example 2 (unequal and zero sample sizes) ###
################################################

# same calculation as above but with a "soft-core" potential and
# illustrating the ability to compute free energies and expectations
# for states with unequal sample sizes including those with
# zero sample sizes (or states that have not been sampled).
# See Tan et al. J. Chem. Phys., 136, 144102 (2012).

rm(list=ls())

# inverse temperature
bet <- 1.0/(0.001986209*300.0)

# negative potential function 
npot.fcn <- function(x, lam)
   -bet*lam*x

# read data (soft core)
lam <- c(0.0, 0.001, 0.002, 0.004, 0.006, 0.008, 0.01, 0.02, 0.06, 0.1,
         0.25, 0.5, 0.75, 0.9, 1.0)
m <- length(lam)

data(ligand2.soft)
lig.data <- ligand2.soft$V1

### unequal and zero sample sizes
size <- c( rep(1000, 5), rep(500, 3), rep(0, 2), rep(1000,5))
subs <- c(rep(TRUE, 5000), rep(c(rep(TRUE,500),rep(FALSE,500)), 3),
          rep(FALSE, 2000), rep(TRUE,5000))
lig.data <- lig.data[subs]

N <- sum(size)

# compute negative potential
neg.pot <- matrix(0, N,m)
for (j in 1:length(lam))
  neg.pot[,j] <- npot.fcn(x=lig.data, lam=lam[j])

# estimate free energies 
out <- uwham(logQ=neg.pot, size=size, fisher=TRUE)

-out$ze/bet + 0.71
sqrt(out$ve)/bet

# block bootstrap for free energies, 
# pretending that the data are generated from independent chains.
# To save time for package checking, this is not run.
#out.boot <- uwham.boot(proc.type="indep", 
#                       block.size=rep(50,m-2), boot.size=100, 
#                       logQ=neg.pot, size=size)
#
#-out.boot$ze/bet + 0.71
#sqrt(out.boot$ve)/bet

#######################################
## example 3 (serial tempering data) ##
#######################################

rm(list=ls())

# inverse temperature
bet <- 1.0/(0.001986209*300.0)

# negative potential function 
npot.fcn <- function(x, lam)
   -bet*lam*x

# lambda states
lam <- c(0.0,0.001,0.002,0.004,0.005,0.006,0.008,0.01,0.02,0.04,
         0.07,0.1,0.25,0.5,0.55,0.6,0.65,0.7,0.75,0.8,
         0.85,0.9,0.95,1.0)
m <- length(lam)

# loads cyclooctanol dataset
data(cyclooctanol)
lig.data <- cyclooctanol$V2

# sample size
N <- length(lig.data)

# state labels based on lambda values
# note that labels=1:m, not 0:(m-1)
state.labels <- factor(cyclooctanol$V1, labels=1:m)

# compute negative potential
neg.pot <- matrix(0, N,m)
for (j in 1:m)
  neg.pot[,j] <- npot.fcn(x=lig.data, lam=lam[j])

# estimate free energies, note that size=NULL because label is given
out <- uwham(label=state.labels, logQ=neg.pot, fisher=TRUE)

# free energies as a function of lambda, 0.36 kcal/mol is a standard
# state correction
-out$ze/bet + 0.36
sqrt(out$ve)/bet

# block bootstrap for free energies, note that proc.type="serial"
# for simulated tempering data.
# To save time for package checking, this is not run.
#out.boot <- uwham.boot(proc.type="serial", block.size=10, boot.size=100, 
#                       label=state.labels, logQ=neg.pot)
#
#-out.boot$ze/bet + 0.36
#sqrt(out.boot$ve)/bet
# }