opensmog 1.3

Structure-based Models for Biomolecules using OpenMM

Documentation | Install | Tutorials

Overview

OpenSMOG is a Python library for performing molecular dynamics simulations using Structure-Based Models. OpenSMOG uses the OpenMM. Python API, which supports a wide variety of potential energy functions, including those that are commonly employed in C-alpha and all-atom models. While it is possible to use this library in a standalone fashion, it is expected that users will generate input files using the SMOG2 software (version 2.4, or later, with the flag -OpenSMOG). Details on how to generate OpenSMOG-compatible force fields files can be found in the SMOG2 User Manual.

Citation

When using OpenSMOG and SMOG2, please use the following references.

Installation

The OpenSMOG library can be installed via conda or pip, or compiled from source (GitHub).

Install via conda

The code below will install OpenSMOG from conda-forge.

conda install -c conda-forge OpenSMOG

Install via pip

The code below will install OpenSMOG from PyPI.

pip install OpenSMOG

OpenMM

The OpenSMOG library uses OpenMM API to run the molecular dynamics simulations. While the above methods should automatically install OpenMM, you can find additional installation options on the OpenMM page..

The following libraries are required for installing OpenSMOG:

• Python (>=3.6)

• NumPy (>=1.14)

• lxml (>=4.6.2)

Installing/Configuring SMOG2

The inputs required for OpenSMOG simulations can be generated using SMOG 2 (version 2.4 and later). For a description of the various ways in which you may access SMOG 2 (e.g. Docker/Singularity container, conda, etc), see the README file in the SMOG 2 GitHub repo.

Resources

• Reference Documentation: Examples, tutorials, and class details.

• Installing OpenSMOG: Instructions for installing OpenSMOG.

• Installing SMOG2: Instructions for installing SMOG2.

• Issue tracker: Report issues/bugs or request features.