FultonMarket

Fully integrated replica exchange simulation modules.

Environment

For preparation of a environment, please refer to openmmtool installation instructions. Dependencies:

• openmmtools (0.25.2)
• mdtraj (1.11.0)
• scikit-learn (1.7.2)
• seaborn (0.13.2)
• jax (see GPU instructions)

Types of Simulation

Parallel Tempering

Parallel Tempering is powered by openmmtools

Description of Scripts:

• FultonMarket.py: Wrapper that runs shorter replica exchange simulations to properly manage disk space, storage considerations, and continuation of experiments.
• Randolph.py: Powers the simulation. Includes options to add interpolation of thermodyanmic states to improve swapping.
• RUN_FULTONMARKET.py Executable to run/resume simulations. To see how to execute, type the following into the console.

$ python RUN_FULTONMARKET.py --help

Parallel Tempering Analysis

Analysis modules are built into this repo.

Description of Scripts:

• FultonMarketAnalysis.py: Makes analysis objects to analyze and resample FultonMarket experiments.
• RESAMPLE.py: Executable to perform importance resampling to acquire trajectories from FultonMarket experiments. To see how to execute, type the following into the console.

$ python ./FultonMarket/analysis/RESAMPLE.py --help