Trimem

Trimem is a python package for the Monte Carlo simulation of lipid membranes according to the Helfrich theory ¹.

Installation

Trimem can be installed using pip:

 git clone --recurse-submodules https://github.com/bio-phys/trimem.git
 pip install trimem/

We suggest the installation using the --user flag to pip. Alternatively, we recommend to consider the usage of virtual environments to isolate the installation of trimem, see, e.g., here.

Dependencies

Trimem builds upon the generic mesh data structure OpenMesh, which is included as a submodule that is pulled in upon git clone via the --recurse-submodules flag.

For the efficient utilization of shared-memory parallelism, trimem makes use of the OpenMP application programming model (>= v4.5) and modern C++. It thus requires relatively up-to-date compilers (supporting at least C++17).

If not already available, the following python dependencies will be automatically installed:

• numpy
• scipy
• h5py
• meshio

Documentation and tests further require:

• autograd
• trimesh
• sphinx
• sphinx-copybutton
• sphinxcontrib-programoutput

Development installation

Unit-tests can be run with

pip install trimem/[tests]
pytest -v tests/

The documentation can be generated with sphinx by

pip install trimem/[docs]
cd doc; make html

Usage

For an introduction to the usage of trimem please refer to the documentation.

Citation

If you use trimem for your scientific work, please consider the citation of Siggel, M. et al².

References

Footnotes

1. Helfrich, W. (1973) Elastic properties of lipid bilayers: Theory and possible experiments. Zeitschrift für Naturforschung C, 28(11), 693-703 ↩

2. Siggel, M. et al. (2022) TriMem: A Parallelized Hybrid Monte Carlo Software for Efficient Simulations of Lipid Membranes. J. Chem. Phys. (in press) (2022); https://doi.org/10.1063/5.0101118 ↩