KineticEnergy#
- class maicos.KineticEnergy(atomgroup: AtomGroup, unwrap: bool = False, refgroup: AtomGroup | None = None, jitter: float = 0.0, concfreq: int = 0, output: str = 'ke.dat', refpoint: str = 'com')[source]#
Bases:
AnalysisBase
Kinetic energy timeseries.
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 (MDAnalysis.core.groups.AtomGroup) – A
AtomGroup
for which the calculations are performed.unwrap (bool) –
When
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 useunwrap=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.refgroup (MDAnalysis.core.groups.AtomGroup) – Reference
AtomGroup
used for the calculation. Ifrefgroup
is provided, the calculation is performed relative to the center of mass of the AtomGroup. Ifrefgroup
isNone
the calculations are performed with respect to the center of the (changing) box.jitter (float) –
Magnitude of the random noise to add to the atomic positions.
A jitter can be used to stabilize the aliasing effects sometimes appearing when histogramming data. The jitter value should be about the precision of the trajectory. In that case, using jitter will not alter the results of the histogram. If
jitter = 0.0
(default), the original atomic positions are kept unchanged.You can estimate the precision of the positions in your trajectory with
maicos.lib.util.trajectory_precision()
. Note that if the precision is not the same for all frames, the smallest precision should be used.concfreq (int) – When concfreq (for conclude frequency) is larger than
0
, the conclude function is called and the output files are written everyconcfreq
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:
- results.trans#
translational kinetic energy (kJ/mol).
- Type:
- results.rot#
rotational kinetic energy (kJ/mol).
- Type:
References