SMOG Tutorials and Examples

Avenues for using SMOG models

The smog-server resource provides many ways in which SMOG models may be designed and deployed. While the first SMOG models were only supported by Gromacs, there is now support provided by NAMD, LAMPPS and OpenMM. In addition, one may generate the models using the smog-server webtool, or the SMOG 2 software package. To help you decide which option is best for your work, we are working to provide step-by-step tutorials that highlight the capabilities of each strategy. Below we list a range of ways in which the resource may be used. Links are provided for worked-out examples, as well as some external resources.
As you get started, you may also find the following introductory material to be helpful:
Using SMOG 2 to simulate complex biomolecular assemblies
Quantifying biomolecular diffusion using a "spherical cow" model

The most basic models

If you are only interested in using a standard SMOG model (i.e. Clementi C-alpha model, or Whitford All-atom model), then there are several approaches you may employ. Depending on the strategy you choose, you may utilize CPU-based, or GPU-based hardware. If your system has fewer than 100k atoms in the model, then GPU options are likely to be beneficial. If you have more than 1M atoms, then CPU-based calculations may be more effective.

The C-alpha model:

The All-atom model:

More elaborate and detailed applications of SMOG models (SMOG 2, only)

While the webtool is useful for the standard SMOG models, anything more interesting requires the use of SMOG 2. SMOG 2 allows for a high level of model customization and extension. If you want maximal versatility, then you should use SMOG 2 with the OpenSMOG libraries for OpenMM. However, there is still a wide range of capabilities when using Gromacs, NAMD and LAMMPS. Since other groups have introduced SMOG-model support in NAMD and LAMMPS, below we only list examples of usage with OpenMM/OpenSMOG and Gromacs. There are more tutorials elsewhere on this site for Gromacs 5. Gromacs 2020 examples are provided with SMOG 2, and we are working to provide updated usage examples for Gromacs 2022. If you find any aspects of these tutorials don't work "out of the box," then let us know.

OpenMM/OpenSMOG usage examples

These examples assume you are using SMOG v2.4.5 and OpenSMOG v1.1.1, or later.

Gromacs usage capabilities

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