Structure-based Models for Biomolecules using OpenMM
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.
When using OpenSMOG and SMOG2, please use the following references.
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
conda install -c conda-forge openmm
The following are libraries required for installing OpenSMOG:
First, download SMOG 2 (v2.4, or later) at smog-server.org
Second, create a new conda environment and activate it (called smog2.4, but name as appropriate):
conda create --name smog2.4 perl
conda activate smog2.4
Next, it is necessary to install 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 (described in the README that comes with SMOG 2).
Then load and test the smog2 installation:
As described in the SMOG 2 manual, it is highly recommended that you also download smog-check and run all checks before using the SMOG 2 software.
Verifying your installation
After you have installed OpenSMOG (and optionally SMOG 2), you can check to see that the code is functioning properly using OpenSMOGcheck. To run the check, you just need to run the following commands (from within python):
from OpenSMOG import SBM
If smog2 is in your path, then this will check compatibility of SMOG2 and OpenSMOG. If smog2 is not in your path, it will simply evaluate the energies for representative models/configurations and compare them to reference values.
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