Nonlocal Electrostatics in Structured Solvents

NESSie.jl is a software package for the popular Julia language, providing efficient numerical solvers for local and nonlocal protein electrostatics computations in structured solvents.

Installation

This version of NESSie.jl requires Julia 1.6 or above. In the Julia shell, switch to the Pkg shell by pressing ] and enter the following command:

pkg> add https://github.com/tkemmer/NESSie.jl

Analogously, the NESSie.jl can be removed at any time using the following command in the Pkg shell:

pkg> rm NESSie

Usage

Modules

All functionality is organized into separate modules:

Module	Description
NESSie	Models and utility functions
NESSie.BEM	Local and nonlocal BEM solvers
NESSie.Format	Input and output file formats
NESSie.TestModel	Test models with analytical solutions

Example

The following Julia code shows how to compute and print the nonlocal reaction field energy of a single Na+ ion (modeled as a spherically-symmetric, vacuum-filled system) in water:

using NESSie
using NESSie.BEM
using NESSie.Format: readoff, readpqr

# I. Create model
model           = readoff("data/born/na.off")
model.charges   = readpqr("data/born/na.pqr")
model.params.εΩ = 1   # dielectric constant for vacuum model
model.params.εΣ = 78  # dielectric constant for water

# II. Apply nonlocal solver
bem = solve(NonlocalES, model)

# III. Apply postprocessor
val = rfenergy(bem)
println("Reaction field energy: $val kJ/mol")

More examples are available in the docs/examples/ directory.

Documentation

A detailed documentation of NESSie.jl is available online.

You can also build the same documentation manually using the following command in the docs/ directory:

shell> julia make.jl

Please note that this additionally requires the Documenter.jl package to be installed. This can be achieved by using the following command in the Pkg shell:

pkg> add Documenter

After the build process has finished successfully, the documentation can be found in the docs/build/ directory.

Testing

NESSie.jl provides tests for most of its functions. You can run the test suite with the following command in the Pkg shell:

pkg> test NESSie

Tools

NESSie.jl ships with the following extra tools:

• Converter.jl, a simple Julia script to convert surface and volume meshes into different formats
• Mesher, a wrapper application for the GAMer library to create surface and volume meshes from PDB files

Please refer to the respective tool's README file for more details.

Citing

If you use NESSie.jl in your research, please cite the following publication:

Kemmer, T, Rjasanow, S., Hildebrandt, A (2018). NESSie. jl - Efficient and Intuitive Finite Element and Boundary Element Methods for Nonlocal Protein Electrostatics in the Julia Language. Journal of Computational Science 28, 193-203.

If you use our implicit representations and solvers (solve_implicit), please also cite:

Kemmer, T (2021). Space-efficient and exact system representations for the nonlocal protein electrostatics problem. Ph. D. thesis, Johannes Gutenberg University Mainz. Mainz, Germany.

Citations items for BibTeX can be found in CITATION.bib.