Installation

Installing OpenSMOG

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. OpenMM may be installed from the conda-forge channel:

conda install -c conda-forge openmm

The following libraries are required when installing OpenSMOG:

Installing SMOG2

The input files for OpenSMOG simulations are generated using SMOG2 (version 2.4, or newer). Here, there is a quick installation guide based on conda (Linux and Windows-WSL only). Alternate installation options are described in the SMOG2 manual.

First, create a new environment and activate it:

conda create --name smog2.4 perl

conda activate smog2.4

Next, it is necessary to instal a few Perl modules (a complete list of modules is in the SMOG2 README file):

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'

Enter the Perl and smog2 paths in the configure.smog2 file.

Then load and test your smog2 configuration:

source configure.smog2

./test-config

It is also STRONGLY recommended that you download smog-check (available at smog-server.org) and run all tests before using smog2 for production calculations.