HybridMC: Hybrid Monte Carlo Protein Folding

HybridMC simulates the event-driven dynamics of coarse-grained protein folding. The entropy and mean first passage times (MFPT) of each bond forming or breaking event are calculated, and the Markov transition rate matrix is constructed. The average time needed to fold to the protein's native state, starting from the unfolded state, is evaluated under two conditions.

This is the wang_landau plugin that is used within that program

For more information, see the publication or the preprint.

Directories

See top level comment in each file for more details as to what each file does. Some top level comments also contain examples of how to run each file, if complicated.

• src: C++ source code for HybridMC program

C++ Program Details

Prerequisite Software

• C++17 compiler with support for C++20 bit library

  see bit operations under C++20 compiler support

  tested with GCC 9.3.0 on CentOS 7.9

• Minimum CMake version is 3.13.1

• Ninja

• HDF5 version 1.10 or later

• Boost

Commands for Compiling

To compile HybridMC Wang landau pybind11 plugin for development and testing:

pip install -e . -vv

Input arguments

This is a python module:

It needs the input JSON configuration file and an optional input HDF5 file in case this is not a layer 0 simulation.

Testing

Run conda install vignesh229::hybridmc

Run examples from hybridmc as per instructions there.