opensmog 0.0.3

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 employing a wide variety of potential forms, including the most commonly employed models such as the C-alpha and All-Atoms. The input files are generated using SMOG2 software with the flag -openSMOG. Details on how to create the files can be found in the SMOG2 User Manual.

Resources

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

• Installing OpenSMOG: Instructions for installing OpenSMOG.

• Installing SMOG2: Instructions for installing SMOG2.

• GitHub repository: Download the OpenMiChroM source code.

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

Citation

When using OpenSMOG to perform chromatin dynamics simulations or analyses, please use this citation.

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

Install OpenMM

The OpenSMOG library uses OpenMM API to run the molecular dynamics simulations. These requirements can be met by installing the following packages from the conda-forge channel:

conda install -c conda-forge openmm

The following are libraries required for installing OpenSMOG:

• Python (>=3.6)

• NumPy (>=1.14)

• ElementTree XML (>=2.2.0)

Installing SMOG2

The inputs OpenSMOG simulations are generated using SMOG2 > 2.4. Here, there is a quick installation guide based on conda.

First, just create a new environment and activate it:

conda create --name smog2.4 perl

conda activate smog2.4

Next, it is necessary an installation of a few Perl modules:

conda install -c bioconda perl-xml-simple perl-xml-libxml java-jdk

conda install -c eumetsat perl-pdl

perl -MCPAN -e 'install XML::Validator::Schema'

Add the Perl and smog2 path into the configure.smog2 file.

Hint

Use the following command line to find out which installed Perl is being used.

which perl

Then load and test the smog2 installation:

source configure.smog2

./test-config