KineticEnergy#

class maicos.modules.kineticenergy.KineticEnergy(atomgroup, output='ke.dat', refpoint='COM')[source]#

Bases: AnalysisBase

Calculate the timeseries of energies.

The kinetic energy function computes the translational and rotational kinetic energy with respect to molecular center (center of mass, center of charge) of a molecular dynamics simulation trajectory.

The analysis can be applied to study the dynamics of water molecules during an excitation pulse. For more details read Elgabarty et al.[1].

Parameters:

  • atomgroup (AtomGroup) – A AtomGroup for which the calculations are performed.

  • refgroup (AtomGroup) –

    Reference AtomGroup used for the calculation.

    If refgroup is provided, the calculation is performed relative to the center of mass of the AtomGroup.

    If refgroup is None the calculations are performed to the center of the (changing) box.

  • unwrap (bool) –

    When unwrap = True, molecules that are broken due to the periodic boundary conditions are made whole.

    If the input contains molecules that are already whole, speed up the calculation by disabling unwrap. To do so, use the flag -no-unwrap when using MAICoS from the command line, or use unwrap = False when using MAICoS from the Python interpreter.

    Note: Molecules containing virtual sites (e.g. TIP4P water models) are not currently supported in MDAnalysis. In this case, you need to provide unwrapped trajectory files directly, and disable unwrap. Trajectories can be unwrapped, for example, using the trjconv command of GROMACS.

  • concfreq (int) – When concfreq (for conclude frequency) is larger than 0, the conclude function is called and the output files are written every concfreq frames

  • refpoint (str) – reference point for molecular center: center of mass (com) or center of charge (coc).

  • output (str) – Output filename.

results.t#

time (ps).

Type:

numpy.ndarray

results.trans#

translational kinetic energy (kJ/mol).

Type:

numpy.ndarray

results.rot#

rotational kinetic energy (kJ/mol).

Type:

numpy.ndarray

References

save()[source]#

Save result.