Density modules#
The density modules of MAICoS are tools for computing density, temperature, and chemical potential profiles from molecular simulation trajectory files. Profiles can be extracted either in Cartesian or cylindrical coordinate systems. Units for the density are the same as GROMACS, i.e. mass, number or charge. See the gmx density manual for details.
From the command line
You can extract a density profile from molecular dynamics
trajectory files directly from the terminal. For this example, we use
the airwater data file of MAICoS. First, go to the directory
cd tests/data/airwater/
then type:
maicos DensityPlanar -s conf.gro -traj traj.trr
Here conf.gro and traj.trr are GROMACS configuration and
trajectory files, respectively. The density profile appears in
a .dat file. You can visualise all the options of the module
DensityPlanar by typing
maicos DensityPlanar -h
From the Python interpreter
In order to calculate the density using MAICoS in a Python environment, first import MAICoS and MDAnalysis:
import MDAnalysis as mda
import maicos
Then create a MDAnalysis universe:
u = mda.Universe('conf.gro', 'traj.trr')
group_H2O = u.select_atoms('type O or type H')
And run MAICoS’ DensityPlanar module:
dplan = maicos.DensityPlanar(group_H2O)
dplan.run()
Results can be accessed from dplan.results. More details are
given in the Tutorials.
Density planar#
Compute partial densities/temperature profiles in the Cartesian systems.
Parameters#
- atomgroupslist[AtomGroup]
a list of
AtomGroupfor which the densities are calculated- densstr
Density: mass, number, charge, temperature.
- dimint
Dimension for binning (x=0, y=1, z=2)
- binwidthfloat
binwidth (nanometer)
- comgroupAtomGroup
Perform the binning relative to the center of mass of the selected group.
- centerbool
Perform the binning relative to the center of the (changing) box.
- mubool
Calculate the chemical potential (requires dens=’number’)
- muoutstr
Prefix for output filename for chemical potential
- temperaturefloat
temperature (K) for chemical potential
- massfloat
Mass (u) for the chemical potential. By default taken from topology.
- zposfloat
position (nm) at which the chemical potential will be computed. By default average over box.
- outputstr
Output filename
- concfreqint
Default number of frames after which results are calculated and files refreshed. If 0 results are only calculated at the end of the analysis and not saved by default.
- verbosebool
Turn on more logging and debugging
Attributes#
- results.zlist
bins
- results.dens_meannp.ndarray
calculated densities
- results.dens_stdnp.ndarray
density standard deviation
- results.dens_errnp.ndarray
density error
- results.mufloat
chemical potential (only if mu=True)
- results.dmufloat
error of chemical potential (only if mu=True)
Density cylinder#
Compute partial densities across a cylinder.
Parameters#
- atomgroupslist[AtomGroup]
A list of
AtomGroupfor which the densities are calculated.- densstr
Density: mass, number, charge, temp
- dimint
Dimension for binning (x=0, y=1, z=2)
- centerstr
Perform the binning relative to the center of this selection string of teh first AtomGroup. If None center of box is used.
- radiusfloat
Radius of the cylinder (nm). If None smallest box extension is taken.
- lengthfloat
Length of the cylinder (nm). If None length of box in the binning dimension is taken.
- binwidthfloat
binwidth (nanometer)
- outputstr
Output filename
- concfreqint
Default number of frames after which results are calculated and files refreshed. If 0 results are only calculated at the end of the analysis and not saved by default.
- verbosebool
Turn on more logging and debugging
Attributes#
- results.rnp.ndarray
bins
- results.dens_meannp.ndarray
calculated densities
- results.dens_mean_sqnp.ndarray
squared calculated density
- results.dens_stdnp.ndarray
density standard deviation
- results.dens_errnp.ndarray
density error