Multiscaling

Bentopy

Bentopy is a workflow for building large-scale models ready for simulation. With bentopy existing structures and experimental evidence can be brought together and assembled to create starting states for large and complex simulations, even on modest workstations.

Bentopy is open-source software developed on our [GitHub repository] and distributed through PyPI (pip).

pip install bentopy

To learn more, take a look at our detailed tutorial and the in-depth documentation on the bentopy wiki.

When using this method, please cite:

Westendorp, M. S. S., Stevens, J. A., Brown, C. M., Dommer, A. C., Wassenaar, T. A., Bruininks, B. M. H., & Marrink, S. J. (2026). Compartment‐guided assembly of large‐scale molecular models with Bentopy. Protein Science, 35(3), e70480. https://doi.org/10.1002/pro.70480

TS2CG: Triangulated Surfaces to Coarse-Grained

TS2CG converts triangulated surfaces (TS) to coarse-grained membrane models for molecular simulation. It also works as a backmapping algorithm from dynamically triangulated surfaces simulations to CG molecular dynamics simulations or to take electron microscopy tomography data and build structures for molecular dynamics simulations.

For more details and to download the latest version, visit the [GitHub repository].

Backward

Backward is a tool to convert a coarse-grained system to united-atom or all-atom resolution. The mapping is done using a library of mapping definitions, which encode the geometric reconstruction. The tool consists of three scripts and a number of CG to fine-grained mapping definition files.

For more details and to download the latest version, visit the [GitHub repository].

When using this method, please cite:

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models Tsjerk A. Wassenaar, Kristyna Pluhackova, Rainer A. Böckmann, Siewert J. Marrink, and D. Peter Tieleman J. Chem. Theory Comput., 10:676-690, 2014. DOI: 10.1021/ct400617g

More extensive information and a tutorial can be found [here].

  • The scripts and mapping definitions for gromacs versions 4 and 5-bead oleoyl lipid chains are combined into a single zip file, which can be downloaded [here].

  • The initram.sh script for version 5 can be downloaded [here].

  • The script for gromacs versions 5 and higher and the mapping files for the amino acid residues and nucleobases are combined into a single zip file, which can be downloaded [here].