Tools for Analyzing and Debugging (SA)FEP calculations
Project description
SAFEP
See detailed documentation here: https://safep-alchemy.readthedocs.io/en/latest/
SAFEP-related scripts and tools
These scripts and notebooks are broadly applicable to FEP analysis.
Sample Notebooks:
- AlternativeParser_nBAR uses less RAM to read large fepout files. Rarely useful unless each fepout file is extremely large.
- BAR_Estimator_Basic: General use FEP analysis. Includes cumulative dG estimates, error estimates, and measures of convergence.
- BAR_Estimator_Expanded: Extendend functionality including bootstrapped error estimates, kernel estimation of dL distributions, and more.
- Batch_Basic: Like BAR_Estimator_Basic but designed for multiple replicas of the same calculation.
Installation:
- Clone this repository
- Enter the repository directory
- Run
pip install .
OR
- Run
pip install git+https://github.com/BranniganLab/safep.git
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