pmx_NCMC

Add replica exchange (ref1) to pmx free energy calculation. The more general form of replica exchange is nonequilibrium candidate Monte Carlo (NCMC) (ref2). This python package is an IO based implementation of replica exchange for pmx-style free energy calculation.

1. Installation

1.1 Create a conda/mamba env

mamba create -n pmx_NCMC python=3.11 pymbar-core numpy pandas matplotlib -c conda-forge
mamba activate  pmx_NCMC  # mambda works the same as conda

1.2 Pip install package

git clone https://github.com/huichenggong/pmx_NCMC.git
pip install .

1.X Remove environment

mamba remove -n pmx_NCMC --all

2. Example

2.1 Dihedral rotation of 2-pentene

Please check the test/2-pentene for more detail

2.2 Solvation free energy of $K^+$ in water

Please check test/Charmm-K/ for more detail

3. Theory

4. Reference

(1) Ballard, A. J.; Jarzynski, C. Replica Exchange with Nonequilibrium Switches. Proc. Natl. Acad. Sci. 2009, 106 (30), 12224–12229. https://doi.org/10.1073/pnas.0900406106.
(2) Nilmeier, J. P.; Crooks, G. E.; Minh, D. D. L.; Chodera, J. D. Nonequilibrium Candidate Monte Carlo Is an Efficient Tool for Equilibrium Simulation. Proc. Natl. Acad. Sci. 2011, 108 (45). https://doi.org/10.1073/pnas.1106094108.

MilesYyh/pmx_NCMC