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.

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.DensityPlanar(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
DensityPlanar	Compute partial densities/temperature profiles in the Cartesian systems.
DensityCylinder	Compute partial densities across a cylinder.
EpsilonBulk	Compute dipole moment fluctuations and static dielectric constant.
EpsilonPlanar	Calculate planar dielectric profiles.
EpsilonCylinder	Calculate cylindrical dielectric profiles.
DielectricSpectrum	Compute the linear dielectric spectrum.
Saxs	Compute SAXS scattering intensities.
Diporder	Calculate dipolar order parameters.
Debyer	Calculate scattering intensities using the debye equation. The debyer library needs to be downloaded and build.
DipoleAngle	Calculate angle timeseries of dipole moments with respect to an axis.
KineticEnergy	Calculate the timeseries of energies.
Velocity	Analyse mean velocity.