README.md

Coarse-grained Simulation using OpenMM

Introduction

This project contains the source code that reproduces the data of the following two papers:

• Wang, Yanming, and Charles L. Brooks III. "Enhanced Sampling Applied to Modeling Allosteric Regulation in Transcription." The Journal of Physical Chemistry Letters 10.19 (2019): 5963-5968.

• Wang, Yanming, and Charles L. Brooks. "Electrostatic Forces Control the Negative Allosteric Regulation in a Disordered Protein Switch." The Journal of Physical Chemistry Letters (2020).

This project contains C++ code running coarse-grained model simulations based on OpenMM (http://openmm.org/).
Now it supports the Electrostatics Inclusive Karanicolas-Brooks (EIKB) Gō model (Karanicolas, John, and Charles L. Brooks III. Protein Science 11.10 (2002): 2351-2361.)

The main feature of this project is that it supports Hamiltonian replica exchange method with highly flexible Hamiltonian by utilizing the flexible OpenMM API.