TensorFlow Optimizer of the Analytical Free Energy Model of Molecular Binding

A class based on TensorFlow for the Maximum Likelihood optimization of the analytic model for the free energy of molecular binding.

Contributors:

Denise Kilburg, dmkilburg@gmail.com

Emilio Gallicchio, egallicchio@brooklyn.cuny.edu

Solmaz Azimi, solmaz.azimi@brooklyn.cuny.edu

References:

1. Denise Kilburg and Emilio Gallicchio. Analytical Model of the Free Energy of Alchemical Molecular Binding. J. Chem. Theory Comput. 14, 6183–6196 (2018) doi:10.1021/acs.jctc.8b00967 pdf of submitted manuscript

Examples

From Alchemical Transformations for Single-Step Hydration Free Energy Calculations. arXiv:2005.06504 (2020)

To employ with the most recent version of AToM

Leg is specified as either 1 or 2

For inspection instead of lambda state, designate stateID

Usage:

python femodel_tf_optimizer-linear_AToM.py -o -l 1 -d data/h2o_explicit_AToM.dat

Inspection:

python femodel_tf_optimizer-linear_AToM.py -r -l 1 -s 10 -d data/h2o_explicit_AToM.dat

Restart Optimization:

python femodel_tf_optimizer-linear_AToM.py -r -o -n 1000 -l 1 -d data/h2o_explicit_AToM.dat

Hydration of 1-naphthol (linear alchemical potential)

Usage:

python femodel_tf_optimizer-linear-example.py -h

Inspection:

python femodel_tf_optimizer-linear-example.py -l 0.267 -d data/water-droplet-1-naphthol-linear/repl.cycle.potE.temp.lambda.ebind.lambda1.lambda2.alpha.u0.w0.dat

Optimization:

python femodel_tf_optimizer-linear-example.py -o -c 10 -n 10 -d data/water-droplet-1-naphthol-linear/repl.cycle.potE.temp.lambda.ebind.lambda1.lambda2.alpha.u0.w0.dat

Restart optimization:

python femodel_tf_optimizer-linear-example.py -r -o -c 10 -n 10 -d data/water-droplet-1-naphthol-linear/repl.cycle.potE.temp.lambda.ebind.lambda1.lambda2.alpha.u0.w0.dat

Hydration of 1-naphthol (integrated logistic alchemical potential)

Usage:

python femodel_tf_optimizer-ilog-example.py -h

Inspection:

python femodel_tf_optimizer-ilog-example.py -l 0.267 -d data/water-droplet-1-naphthol-ilog/repl.cycle.potE.temp.lambda.ebind.lambda1.lambda2.alpha.u0.w0.dat

Optimization:

python femodel_tf_optimizer-ilog-example.py -o -c 10 -n 10 -d data/water-droplet-1-naphthol-ilog/repl.cycle.potE.temp.lambda.ebind.lambda1.lambda2.alpha.u0.w0.dat