Step 1: Prepare a simulation

Before running a simulation, you will need to define a force field. The SMOG resource provides two different approaches.

SMOG Webtool: If you want to use the most basic forms of these models, then the webtool will probably be sufficient. Force fields generated with the webtool may be used in Gromacs, or unofficial modified versions of Gromacs. Some of the models may also be used with NAMD, OpenMM, or LAMMPS.

SMOG 2: SMOG 2 is a downloadable version of the software, and it is far more comprehensive than the webtool. One can define almost any concievable structure-based model, for systems of arbitrary molecular composition, complexity, energetic representation (e.g. ions and electrostatics) and size. Also, SMOG 2 provides support for the OpenSMOG library, which allows all SMOG models to be simulated with OpenMM. SMOG 2 also generates force fields that are compatible with Gromacs, NAMD and LAMMPS.

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