This extension makes it possible to create coarse-grained models for the MARTINI force field.

The extension uses Martinize2 and Vermouth to create coarse-grained representations of systems.

Documentation

Tutorial: Creating coarse-grained models for the MARTINI force field using Martinize2.

Here is how to use Martinize2 in SAMSON:

1. Load in SAMSON a structure for which you would like to create its coarse-grained representation.
2. In Martinize2, choose a folder where results should be saved.
3. Select the structure in the document and then, in Martinize2, click on "Set".
4. Modify the Martinize2 options, if necessary.
5. Click "Create coarse-grained models".
6. You should see the progress in the log output and the results should appear in a timestamped subfolder in the chosen results folder.

References

[1] Peter C. Kroon, Fabian Grünewald, Jonathan Barnoud, Marco van Tilburg, Paulo C. T. Souza, Tsjerk A. Wassenaar, Siewert-Jan Marrink. Martinize2 and Vermouth: Unified Framework for Topology Generation.

[2] P.C.T. Souza, R. Alessandri, J. Barnoud, S. Thallmair, I. Faustino, F. Grünewald, et al., Martini 3: a general purpose force field for coarse-grained molecular dynamics, Nat. Methods. 18 (2021) 382–388.