maicos 0.11.1

Analyse molecular dynamics simulations of interfacial and confined systems.

MAICoS

MAICoS stands for Molecular Analysis for Interfacial and Confined Systems. It is an object-oriented Python toolkit for analyzing the structure and dynamics of interfacial and confined fluids from molecular simulations. Combined with MDAnalysis, MAICoS enables the extraction of density profiles, dielectric constants, structure factors, and transport properties from trajectory files generated by LAMMPS, GROMACS, CHARMM, or NAMD simulations. MAICoS is open source and released under the GNU General Public License v3.0.

MAICoS is designed both for beginners in molecular simulations with no prior Python experience— offering a descriptive Command Line Interface (CLI)—and for experienced users who can use the Python API for day-to-day analysis or build their own workflows for interfacial and confined systems.

Stay up to date with MAICoS news by following us on X. If you encounter any issues, report them on GitHub, or join our developer community on Discord to discuss features and improvements.

Basic Example

Here is a simple example showing how to use MAICoS to extract a density profile from a molecular dynamics simulation. The files conf.gro and traj.trr correspond to output files from a GROMACS simulation. In a Python environment, type:

import MDAnalysis as mda
import maicos

u = mda.Universe("conf.gro", "traj.trr")
dplan = maicos.DensityPlanar(u.atoms).run()

The density profile is stored in dplan.results.profile, and the corresponding bin positions are available in dplan.results.bin_pos.

Documentation

For details, tutorials, and examples, visit our official documentation. We also provide the latest documentation for the current development version of MAICoS.

Installation

Install MAICoS using pip:

pip install maicos

Or with conda from conda-forge:

conda install -c conda-forge maicos

List of Analysis Modules

Currently, MAICoS supports the following analysis modules (alphabetically):

Module	Description
DensityCylinder	Cylindrical partial density profiles
DensityPlanar	Cartesian partial density profiles
DensitySphere	Spherical partial density profiles
DielectricCylinder	Cylindrical dielectric profiles
DielectricPlanar	Planar dielectric profiles
DielectricSpectrum	Linear dielectric spectrum
DielectricSphere	Spherical dielectric profiles
DipoleAngle	Time series of dipole moment angles
DiporderCylinder	Cylindrical dipolar order parameters
DiporderPlanar	Planar dipolar order parameters
RDFDiporder	Spherical radial distribution function between dipoles
DiporderSphere	Spherical dipolar order parameters
DiporderStructureFactor	Structure factor for dipoles
KineticEnergy	Time series of kinetic energies
PDFCylinder	Cylindrical shell-wise 1D pair distribution functions
PDFPlanar	Slab-wise planar 2D pair distribution functions
Saxs	Small-angle X-ray scattering (SAXS): structure factors and scattering intensities
TemperaturePlanar	Temperature profiles in a Cartesian geometry
VelocityCylinder	Cylindrical velocity profiles
VelocityPlanar	Velocity profiles in a Cartesian geometry

Contributors

Thanks to all contributors who make MAICoS possible: