UWHAM (version 1.0)

uwham.phi: Unbinned weighted histogram analysis method (UWHAM) for estimating expectations

Description

This function implements UWHAM for estimating expectations for multiple distributions (such as multiple generalized ensembles) as described in Tan et al. (2012).

Usage

uwham.phi(phi, state, out.uwham, fisher = TRUE)

Arguments

phi

A vector of function (or observable) values on the pooled sample.

state

A vector of indices between 1 to M for the thermodynamic states under which expectations are to be computed.

out.uwham

The output of uwham.

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

phi

The vector of estimated expectations.

phi.v

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

phi.V

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

Details

The implementation is directly based on Tan et al. (2012). See the details for uwham.

References

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 {
#See the examples for uwham().

# }