Forcefields

Force fields play an important role in membrane simulations, as they define the naming conventions and structural details for lipids and other membrane components. twodanalysis currently supports the CHARMM and AMBER force fields. However, the package was designed to be as general as possible, so many features will still work with other force fields if the guidelines in When problems arise are followed.

We are actively working to extend full support to additional force fields in future releases. In the meantime, we encourage users to open issues on our GitHub page if their force field is not recognized or if specific functionality is needed.

We have introduced a simple way to specify the forcefield. You should add the flag forcefield with either “amber” or “charmm” when initializing the Cumulative2D, Voronoi2D or PackingDefects objects, as follows.

For amber:

memb1 = Cumulative2D(forcefield = "amber")
memb2 = Voronoi2D(forcefield = "amber")
memb3 = PackingDefects(forcefield = "amber")

If you have any problems using the amber forcefield, please refer to When problems arise.

For charmm:

memb1 = Cumulative2D(forcefield = "charmm")
memb2 = Voronoi2D(forcefield = "charmm")
memb3 = PackingDefects(forcefield = "charmm")

If you have any problems using the amber forcefield, please refer to When problems arise.

Note

The default forcefield is charmm, if you do not specify the forcefield, charmm will be used automatically.

Other forcefields:

If you are using a different forcefield, please refer to When problems arise.

References

• Ramirez, R. X., Bosch, A. M., Pérez, R., Guzman, H. V., & Monje, V. (2025). 2Danalysis: A toolbox for analysis of lipid membranes and biopolymers in two-dimensional space. Biophysical Journal.