- class maicos.modules.kineticenergy.KineticEnergy(atomgroup, output='ke.dat', refpoint='COM')[source]#
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..
atomgroup (AtomGroup) – A
AtomGroupfor which the calculations are performed.
refgroup (AtomGroup) –
AtomGroupused for the calculation.
If refgroup is provided, the calculation is performed relative to the center of mass of the AtomGroup.
If refgroup is
Nonethe calculations are performed to the center of the (changing) box.
unwrap (bool) –
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-unwrapwhen using MAICoS from the command line, or use
unwrap = Falsewhen 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
trjconvcommand 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 (
output (str) – Output filename.
translational kinetic energy (kJ/mol).
rotational kinetic energy (kJ/mol).