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.

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 a water slab in vacuum that was simulated in this case using the GROMACS simulation package. In a Python environment, type:

import MDAnalysis as mda
import maicos
u = mda.Universe('conf.gro', 'traj.trr')
grpH2O = u.select_atoms('type O or type H')
dplan = maicos.density_planar(grpH2O)
dplan.run()

Results can be accessed from dplan.results.

Installation

Python3 and a C-compiler are needed to build the underlying libraries.

Using pip

If you have root access, install the package for all users by typing in a terminal:

pip3 install numpy
pip3 install maicos

Alternatively, if you don’t have special privileges, install the package in your home directory by using the --user flag.

List of analysis modules

Module Name	Description
density_planar	Compute partial densities/temperature profiles in the Cartesian systems.
density_cylinder	Compute partial densities across a cylinder.
epsilon_bulk	Compute dipole moment fluctuations and static dielectric constant.
epsilon_planar	Calculates a planar dielectric profile.
epsilon_cylinder	Calculate cylindrical dielectric profiles.
dielectric_spectrum	Computes the linear dielectric spectrum.
saxs	Compute SAXS scattering intensities.
diporder	Calculation of dipolar order parameters.
debyer	Calculate scattering intensities using the debye equation. The debyer library needs to be downloaded and build.
dipole_angle	Calculate angle timeseries of dipole moments with respect to an axis.
kinetic_energy	Calculate the timeseries of energies.
velocity	Mean velocity analysis.