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Analyse molecular dynamics simulations of interfacial and confined systems.

Project description

MAICoS

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:

Module Name

Description

DensityPlanar

Compute cartesian partial density profiles

DensityCylinder

Compute cylindrical partial densitiy profiles

DensitySphere

Compute spherical partial density profiles

TemperaturePlanar

Compute temperature profiles in a cartesian geometry

DielectricPlanar

Compute planar dielectric profiles

DielectricCylinder

Compute cylindrical dielectric profiles

DielectricSphere

Compute spherical dielectric profiles

DielectricSpectrum

Compute the linear dielectric spectrum

Saxs

Compute small angle X-Ray scattering intensities (SAXS)

DiporderPlanar

Compute planar dipolar order parameters

DiporderCylinder

Compute cylindrical dipolar order parameters

DiporderSphere

Compute spherical dipolar order parameters

PDFPlanar

Compute slab-wise planar 2D pair distribution functions

PDFCylinder

Compute cylindrical shell-wise 1D pair distribution functions

DipoleAngle

Compute angle timeseries of dipole moments

KineticEnergy

Compute the timeseries of energies

VelocityPlanar

Compute the velocity profile in a cartesian geometry

VelocityCylinder

Compute the cartesian velocity profile across a cylinder

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