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 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:
Python (>=3.6)
NumPy (>=1.14)
ElementTree XML (>=2.2.0)
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. Please, download SMOG2 package at the SMOG-SERVER.
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.