OpenSMOG with SMOG 2

Simulating SMOG models in OpenMM

Manuscripts   Manual   Force Field Repo   OpenSMOG

Beginning with SMOG v2.4, it is possible to create force fields that are written specifically for use with OpenMM. This is enabled through use of the OpenSMOG module, which is provided by the smog-server team. SMOG 2 and OpenSMOG have been co-designed for integrated use. In addition to allowing for utilization of OpenMM GPU-accelerated libraries, the OpenSMOG option of SMOG 2 allows one to design highly customized SMOG models. Essentially, any pair-wise potential energy function may be used for native contacts (v1.0 and later) and nonbonded parameters (v1.1 and later). Future releases are planned that will allow for additional customizations.

Documentation and Download

For details on download, installation and usage of OpenSMOG, see the manuscript, SMOG 2 manual or official OpenSMOG documentation.

OpenSMOG v1.1.1 is now available! For best performance, use with SMOG v2.4.5.

OpenSMOG may be downloaded in the following ways:

  • Conda
  • PIP
  • Docker - For demonstrative/educational purposes, only. Also contains SMOG 2.

OpenSMOG-check (test suite)

It is strongly recommended that you verify your installations of OpenSMOG and SMOG2 are compatible. To ensure the two packages are working well together, we have prepared a short set of tests (OpenSMOG-check). If SMOG 2 is not in your path, then the script will simply check to make sure your configuration of OpenSMOG is reproducing some standard energies. In addition to running OpenSMOG-check, it is recommended that you also download and run smog-check, to ensure all aspects of SMOG2 are working properly. If you encounter any issues, please let us know.

Note: Starting with v1.1.1, opensmogcheck has been integrated with the OpenSMOG distribution, so it is automatically available when OpenSMOG is installed.

OpenSMOG-check version SMOG 2 version md5 (.tgz file)
1.1 >=2.4.4 c3972ac77c5abaa5ae8fdb2725a95a71
1.0.4 2.4.1 d51bbfcae8211ebbdb766f306062726e

OpenSMOG-check usage instructions can be found in the README file.

This resource is provided by the Center for Theoretical Biological Physics.
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Page created and maintained by Jeff Noel and Paul Whitford