Free Energy Based Identification of Solvation Sites (FEBISS)

Installation

FEBISS can be installed using pip (pip3) once the repository has been cloned:

git clone https://github.com/PodewitzLab/FEBISS.git
pip install ./FEBISS/

A non super user can install the package using a virtual environment, or the --user flag.

A manual with detailed instructions can be found in the Github repo.

Prerequisites

Basic Requirements

FEBISS is expected to run on Linux systems and the following programs/packages are required:

• Python3
• Git
• GCC >= v7.0.0

Febiss Python Package

The main Python package called FEBISS requires only basic additional packages, which will be automatically installed when installing FEBISS, using pip. These packages are listed in the file requirements.txt.

C++ Requirements

To run analyses of trajectories the open-source software CPPTRAJ modified with the GIGIST repository is used. These dependencies are not necessary for the installation of FEBISS, but rather FEBISS provides a script to set-up these dependencies via

We reccomend the use of CUDA to speed up the GIST calculations. In this case, make sure that cuda is installed on your system and the the CUDA_HOME variable points to your CUDA installation.

febiss_setup

Please be aware that CPPTRAJ may require libraries that cannot be installed via FEBISS, but have to be installed by the user first. CPPTRAJ makes use of the following libraries:

• NetCDF
• BLAS
• LAPACK
• Gzip
• Bzip2
• Parallel NetCDF (-mpi build only, for NetCDF trajectory output in parallel)
• CUDA (-cuda build only)
• FFTW (mostly optional; required for PME functionality and very large FFTs)

We therefore recommend to install some basic libraries via

sudo apt-get install libblas-dev liblapack-dev libbz2-dev libnetcdf-dev

Should you encounter difficulties in the installation of CPPTRAJ, we refer to the README of the GIGIST and CPPTRAJ repositories.

Basic Usage

If you installed FEBISS and its dependencies febiss_setup, you can use FEBISS to analyse trajectories for water placements, plot the data and select the waters you want to further investigate within a bar chart.

To get a list of all available options and a useful input file, you can call

febiss_settings

This will place the file all-settings.yaml in your current directory. This input file requires only 2 alterations to be a valid input file. You have to give the name of your topology file and the base name of your trajectory file(s). Along those 2 mandatory settings you find all other available settings both for the GIST analysis and the plotting of the retrieved data. Once you performed the analysis, you can also skip this step and directly plot the data. The analysis and plotting are done via calling the main program along with the yaml input file:

febiss all-settings.yaml