maicos 0.6

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.

For details, tutorials, and examples, please have a look at our documentation.

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
DipoleAngle	angle timeseries of dipole moments with respect to an axis
KineticEnergy	energy timeseries.
Velocity	mean velocity profile in a cartesian geometry