| obj.fcn {UWHAM} | R Documentation |
The objective function for UWHAM
Description
This function computes the objective function, its gradient and its hessian matrix for UWHAM.
Usage
obj.fcn(ze, logQ, size, base)
Arguments
ze |
A vector of log-normalizing constants (or free energies) for the sampled thermodynamic states. |
logQ |
The matrix of log of unnormalized density ratios for the sampled thermodynamic states over the baseline. |
size |
A vector giving the individual sample sizes for the sampled thermodynamic states. |
base |
The baseline index. |
Details
The objective function is convex as discussed in Tan et al. (2012). See also Gill et al. (1998) for related results on biased sampling models.
Value
value |
The value of the objective function. |
gradient |
The gradient of the objective function. |
hessian |
The hessian matrix of objective function. |
References
Gill, R., Vardi, Y., and Wellner, J. (1998) "Large sample theory of empirical distributions in biased sampling models," Annals of Statistics, 16, 1069–1112.
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.