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.

Gromacs: SMOG models will work with any version of Gromacs (>v3). 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.

OpenMM: There are two ways to run SMOG models in OpenMM. If you are using the default all-atom SMOG model, then you can probably just follow the introduction to using SMOG models in OpenMM that is available from the Grossfield group. If you need more flexibility in how you may define a SMOG model, then you can use SMOG (v2.4 and later) with the OpenSMOG module for OpenMM. OpenSMOG frees the user of specific functional forms, and thereby greatly increases the range of models that can be simulated with OpenMM. See SMOG 2 users manual for details.

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.
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