MAICoS#

_images/logo_MAICOS_square.png

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.

Due to ongoing major restructuring work, some modules are currently not working correctly (transport and dielectric analysis). Use `v0.3` for your work as shown in the Installation directions.

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==0.3

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

partial densities profiles in a cartesian geometry

TemperaturePlanar

temperature profiles in a cartesian geometry

ChemicalPotentialPlanar

chemical potential in a cartesian geometry

DensityCylinder

partial densities across a cylinder

EpsilonPlanar

planar dielectric profiles

EpsilonCylinder

cylindrical dielectric profiles

DielectricSpectrum

linear dielectric spectrum of a bulk system

Saxs

SAXS scattering intensities

Diporder

dipolar order parameters

RDFPlanar

planar radial distribution function

Debyer

scattering intensities using the debye equation. The debyer library needs to be downloaded and build

DipoleAngle

angle timeseries of dipole moments with respect to an axis

KineticEnergy

energy timeseries.

Velocity

mean velocity profile in a cartesian geometry