Kinetic energy tutorial

Here we analyse a box of water molecules. To follow this tutorial, the data test files kineticenergy of MAICoS are needed. You can obtain them by cloning MAICoS repository:

git clone git@gitlab.com:maicos-devel/maicos.git

Simulation details - The system contains around 500 water molecules simulated for 200 ps in the NVE ensemble. Periodic boundary conditions were employed in all directions, long range electrostatics were modelled using the PME method, and the LINCS algorithm was used to constraint the H-Bonds.

Option 1: from the Python interpreter

First, let us ignore unnecessary warnings:

import warnings
warnings.filterwarnings("ignore")

Then, import MAICoS, NumPy, MDAnalysis, and PyPlot:

import maicos
import numpy as np
import MDAnalysis as mda
import matplotlib.pyplot as plt
from matplotlib.ticker import AutoMinorLocator

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In [2], line 1
----> 1 import maicos
      2 import numpy as np
      3 import MDAnalysis as mda

File ~/checkouts/readthedocs.org/user_builds/maicos/envs/v0.5/lib/python3.10/site-packages/maicos/__init__.py:36
     29 from .modules.density import DensityPlanar, DensityCylinder
     30 from .modules.epsilon import (
     31     EpsilonBulk,
     32     EpsilonPlanar,
     33     EpsilonCylinder,
     34     DielectricSpectrum
     35 )
---> 36 from .modules.structure import Saxs, Debye, Diporder
     37 from .modules.timeseries import DipoleAngle, KineticEnergy
     38 from .modules.transport import Velocity

File ~/checkouts/readthedocs.org/user_builds/maicos/envs/v0.5/lib/python3.10/site-packages/maicos/modules/structure.py:24
     18 from .. import tables
     19 from ..decorators import (
     20     make_whole,
     21     set_planar_class_doc,
     22     set_verbose_doc,
     23 )
---> 24 from ..lib import sfactor
     25 from ..utils import check_compound, savetxt
     27 logger = logging.getLogger(__name__)

ImportError: dynamic module does not define module export function (PyInit_sfactor)

and set a few parameters for plotting purpose:

fontsize = 25
font = {'family': 'sans', 'color':  'black',
        'weight': 'normal', 'size': fontsize}
my_color_1 = np.array([0.090, 0.247, 0.560])
my_color_2 = np.array([0.235, 0.682, 0.639])
my_color_3 = np.array([1.000, 0.509, 0.333])
my_color_4 = np.array([0.588, 0.588, 0.588])

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In [3], line 4
      1 fontsize = 25
      2 font = {'family': 'sans', 'color':  'black',
      3         'weight': 'normal', 'size': fontsize}
----> 4 my_color_1 = np.array([0.090, 0.247, 0.560])
      5 my_color_2 = np.array([0.235, 0.682, 0.639])
      6 my_color_3 = np.array([1.000, 0.509, 0.333])

NameError: name 'np' is not defined

Define the path to the kineticenergy data folder of MAICoS:

datapath = "../../../../tests/data/kineticenergy/"

Create a MDAnalysis universe:

u = mda.Universe(datapath+"nve.tpr",
                 datapath+"nve.trr")
atoms = u.atoms

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In [5], line 1
----> 1 u = mda.Universe(datapath+"nve.tpr",
      2                  datapath+"nve.trr")
      3 atoms = u.atoms

NameError: name 'mda' is not defined

Let us print a few information about the trajectory file:

print(f"The number of water molecules is {np.int32(u.atoms.n_atoms/3)}")
timestep = np.round(u.trajectory.dt,2)
print(f"The time interval between the frames is {timestep} ps")
total_time = np.round(u.trajectory.totaltime,2)
print(f"The total simulation time is {total_time} ps")

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In [6], line 1
----> 1 print(f"The number of water molecules is {np.int32(u.atoms.n_atoms/3)}")
      2 timestep = np.round(u.trajectory.dt,2)
      3 print(f"The time interval between the frames is {timestep} ps")

NameError: name 'np' is not defined

Run the MAICOS dipole angle function:

kenergy = maicos.KineticEnergy(atoms)
kenergy.run()

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In [7], line 1
----> 1 kenergy = maicos.KineticEnergy(atoms)
      2 kenergy.run()

NameError: name 'maicos' is not defined

Then extract the kinetic energy:

ke_trans = kenergy.results["trans"]
ke_rot = kenergy.results["rot"]
print(f"The average translational kinetic energy "
      f"is {np.round(np.mean(ke_trans),2)} kJ/mol")
print(f"The average rotational kinetic energy "
      f"is {np.round(np.mean(ke_rot),2)} kJ/mol")

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In [8], line 1
----> 1 ke_trans = kenergy.results["trans"]
      2 ke_rot = kenergy.results["rot"]
      3 print(f"The average translational kinetic energy "
      4       f"is {np.round(np.mean(ke_trans),2)} kJ/mol")

NameError: name 'kenergy' is not defined

Option 2 : from the command line interface

Go to the kineticenergy data folder of MAICoS, then use the maicos command directly from the terminal:

maicos KineticEnergy -s md.tpr -f md.trr -o ke.dat

The output file ke.dat is similar to ke.results and contains the data in columns