maicos 0.9

Analyse molecular dynamics simulations of interfacial and confined systems.

MAICoS is the acronym for Molecular Analysis for Interfacial and Confined Systems. It is an object-oriented python toolkit for analysing the structure and dynamics of interfacial and confined fluids from molecular simulations. Combined with MDAnalysis, MAICoS can be used to extract density profiles, dielectric constants, structure factors, or transport properties from trajectories files, including LAMMPS, GROMACS, CHARMM or NAMD data. MAICoS is open source and is released under the GNU general public license v3.0.

MAICoS is a tool for beginners of molecular simulations with no prior Python experience. For these users MAICoS provides a descriptive command line interface. Also experienced users can use the Python API for their day to day analysis or use the provided infrastructure to build their own analysis for interfacial and confined systems.

Keep up to date with MAICoS news by following us on Twitter. If you find an issue, you can report it on Gitlab. You can also join the developer team on Discord to discuss possible improvements and usages of MAICoS.

Basic example

This is a simple example showing how to use MAICoS to extract the density profile from a molecular dynamics simulation. The files conf.gro and traj.trr correspond to simulation files from a GROMACS simulation package. 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 can be accessed from dplan.results.profile and the position of the bins from dplan.results.bin_pos.

Documentation

For details, tutorials, and examples, please have a look at our documentation. If you are using an older version of MAICoS, you can access the corresponding documentation on ReadTheDocs.

Installation

Install MAICoS using pip with:

pip install maicos

or using conda with:

conda install -c conda-forge maicos

List of analysis modules

Currently, MAICoS supports the following analysis modules in alphabetical order:

Module Name	Description
DensityCylinder	Compute cylindrical partial densitiy profiles
DensityPlanar	Compute cartesian partial density profiles
DensitySphere	Compute spherical partial density profiles
DielectricCylinder	Compute cylindrical dielectric profiles
DielectricPlanar	Compute planar dielectric profiles
DielectricSpectrum	Compute the linear dielectric spectrum
DielectricSphere	Compute spherical dielectric profiles
DipoleAngle	Compute angle timeseries of dipole moments
DiporderCylinder	Compute cylindrical dipolar order parameters
DiporderPlanar	Compute planar dipolar order parameters
RDFDiporder	Spherical Radial Distribution function between dipoles
DiporderSphere	Compute spherical dipolar order parameters
DiporderStructureFactor	Structure factor for dipoles
KineticEnergy	Compute the timeseries of energies
PDFCylinder	Compute cylindrical shell-wise 1D pair distribution functions
PDFPlanar	Compute slab-wise planar 2D pair distribution functions
Saxs	Compute small angle X-Ray structure factors and scattering intensities (SAXS)
TemperaturePlanar	Compute temperature profiles in a cartesian geometry
VelocityCylinder	Compute the cartesian velocity profile across a cylinder
VelocityPlanar	Compute the velocity profile in a cartesian geometry