Step 2: Run a simulation

While the SMOG team provides support for use of these models with Gromacs and OpenMM, we are grateful to other research groups that have ported (and provide support for) SMOG models in additional software package, including NAMD and LAMMPS.

Methods supported by the SMOG Team

OpenSMOG (built on OpenMM): For maximum versatility and excellent performance on GPUs, it is recommended that you use OpenSMOG to perfom your simulations. OpenSMOG is a set of libraries that allows the models generated by SMOG 2 to be performed using the high-performance OpenMM libraries. OpenSMOG supports all of the common SMOG models. In addition, you can use SMOG 2 to design new variants of SMOG models that can be simulated using OpenSMOG (for examples, see the SMOG 2 force field repository). If you would like to try SMOG 2 with OpenSMOG, it is helpful to first try our step-by-step tutorials, which demonstrate some of the capabilities of these tools. The SMOG 2 users manual also has technical details on OpenSMOG usage.

Gromacs: Many types of SMOG models will work with Gromacs. We have tested versions as late as 2020. For descriptions of how to perform a simulation using Gromacs v4 or v5, see our SMOG models in Gromacs page. There is also information available in the SMOG 2 manual.

External Resources

OpenMM (without OpenSMOG): If you are only interested in using the default all-atom SMOG model, then you may be able to simply follow the introduction to using SMOG models in OpenMM that is available from the Grossfield group.

NAMD: Thanks to the Luthey-Schulten group, NAMD supports force fields generated with smog-server or SMOG 2.

LAMMPS: The Micheletti group provides software for converting smog-server and SMOG 2 force fields into a format that is usable with LAMMPS. See SMOG-converter

This resource is provided by the Center for Theoretical Biological Physics.
Please direct questions and comments to info@smog-server.org.
Page created and maintained by Jeff Noel and Paul Whitford