alanyu19/fflip

fflip

Force Field of Lipids Parametrization

A Python package for automation of molecular simulations and optimization of lipid force field parameters.

• Free software: GNU General Public License v3
• Documentation: https://fflip.readthedocs.io.

Features

• ... more to come

Third-party Software

The following third-party software is not required to install fflip. However, a lot of fflip's functionality depends on molecular simulation packages. In order to use program-specific functions, these programs have to be installed.

1. CHARMM (optional): Required for fflip/uachain. Make sure the command charmm can be called from a terminal.
2. OpenMM: Required.
3. openmmtools: Required.
4. mdtraj: Required.
5. Rickflow: Required (https://gitlab.com/Olllom/rickflow/tree/master).

Other comments here.

Getting Started

1. conda create -n fflip python=3.11 (then "conda activate fflip")
2. conda install dask distributed -c conda-forge
3. conda install dask-jobqueue -c conda-forge
4. conda install -c conda-forge openmm
5. conda install -c conda-forge openmmtools
6. conda install -c conda-forge mdtraj
7. Install rickflow (https://gitlab.com/Olllom/rickflow/tree/master)
8. goto fflip and run "python setup.py install" (if a develop mode is preferred, use "python setup.py develop")

You are ready to go!

Tutorials

• Using fflip with OpenMM/CHARMM:
  1. Parameterize alkane/alkene systems (pending): Tutorial1.
  2. Optmization for the CHARMM additive lipid FF: Tutorial2.

Developers' Guide

1. Coding conventions
2. Notes on how to add modules, classes, functions, etc.
3. Contributing to the code
4. Notes to core developers

Related Work

Currently none.

Credits

Find out about the authors here.