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, 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.
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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.
For details, tutorials, and examples, visit our official documentation. We also provide the latest documentation for the current development version of MAICoS.
Install MAICoS using pip:
pip install maicos
Or with conda from conda-forge:
conda install -c conda-forge maicos
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 |
| DielectricSphere | Spherical dielectric profiles |
| DiporderCylinder | Cylindrical dipolar order parameters |
| DiporderPlanar | Planar dipolar order parameters |
| RDFDiporder | Spherical radial distribution function between dipoles |
| DiporderSphere | Spherical dipolar order parameters |
| PDFCylinder | Cylindrical shell-wise 1D pair distribution functions |
| PDFPlanar | Slab-wise planar 2D pair distribution functions |
| TemperaturePlanar | Temperature profiles in a Cartesian geometry |
| VelocityCylinder | Cylindrical velocity profiles |
| VelocityPlanar | Velocity profiles in a Cartesian geometry |
Thanks to all contributors who make MAICoS possible: