Examples

waterdynamics operates around class based analyses. Find examples of their use below. For an explanation of the classes’ outputs, see the outputs page.

HydrogenBondLifetimes

To analyze hydrogen bond lifetime, use MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.lifetime().

See also

MDAnalysis.analysis.hydrogenbonds.hbond_analysis

WaterOrientationalRelaxation

Analyzing water orientational relaxation (WOR) WaterOrientationalRelaxation. In this case we are analyzing “how fast” water molecules are rotating/changing direction. If WOR is very stable we can assume that water molecules are rotating/changing direction very slow, on the other hand, if WOR decay very fast, we can assume that water molecules are rotating/changing direction very fast:

import MDAnalysis
from waterdynamics import WaterOrientationalRelaxation as WOR

u = MDAnalysis.Universe(pdb, trajectory)
select = "byres name OH2 and sphzone 6.0 protein and resid 42"
WOR_analysis = WOR(universe, select, 0, 1000, 20)
WOR_analysis.run()
time = 0
#now we print the data ready to plot. The first two columns are WOR_OH vs t plot,
#the second two columns are WOR_HH vs t graph and the third two columns are WOR_dip vs t graph
for WOR_OH, WOR_HH, WOR_dip in WOR_analysis.timeseries:
      print("{time} {WOR_OH} {time} {WOR_HH} {time} {WOR_dip}".format(time=time, WOR_OH=WOR_OH, WOR_HH=WOR_HH,WOR_dip=WOR_dip))
      time += 1

#now, if we want, we can plot our data
plt.figure(1,figsize=(18, 6))

#WOR OH
plt.subplot(131)
plt.xlabel('time')
plt.ylabel('WOR')
plt.title('WOR OH')
plt.plot(range(0,time),[column[0] for column in WOR_analysis.timeseries])

#WOR HH
plt.subplot(132)
plt.xlabel('time')
plt.ylabel('WOR')
plt.title('WOR HH')
plt.plot(range(0,time),[column[1] for column in WOR_analysis.timeseries])

#WOR dip
plt.subplot(133)
plt.xlabel('time')
plt.ylabel('WOR')
plt.title('WOR dip')
plt.plot(range(0,time),[column[2] for column in WOR_analysis.timeseries])

plt.show()

where t0 = 0, tf = 1000 and dtmax = 20. In this way we create 20 windows timesteps (20 values in the x axis), the first window is created with 1000 timestep average (1000/1), the second window is created with 500 timestep average(1000/2), the third window is created with 333 timestep average (1000/3) and so on.

AngularDistribution

Analyzing angular distribution (AD) AngularDistribution for OH vector, HH vector and dipole vector. It returns a line histogram with vector orientation preference. A straight line in the output plot means no preferential orientation in water molecules. In this case we are analyzing if water molecules have some orientational preference, in this way we can see if water molecules are under an electric field or if they are interacting with something (residue, protein, etc):

import MDAnalysis
from waterdynamics import AngularDistribution as AD

u = MDAnalysis.Universe(pdb, trajectory)
selection = "byres name OH2 and sphzone 6.0 (protein and (resid 42 or resid 26) )"
bins = 30
AD_analysis = AD(universe,selection,bins)
AD_analysis.run()
#now we print data ready to graph. The first two columns are P(cos(theta)) vs cos(theta) for OH vector ,
#the seconds two columns are P(cos(theta)) vs cos(theta) for HH vector and thirds two columns
#are P(cos(theta)) vs cos(theta) for dipole vector
for bin in range(bins):
      print("{AD_analysisOH} {AD_analysisHH} {AD_analysisDip}".format(AD_analysis.graph0=AD_analysis.graph[0][bin], AD_analysis.graph1=AD_analysis.graph[1][bin],AD_analysis.graph2=AD_analysis.graph[2][bin]))

#and if we want to graph our results
plt.figure(1,figsize=(18, 6))

#AD OH
plt.subplot(131)
plt.xlabel('cos theta')
plt.ylabel('P(cos theta)')
plt.title('PDF cos theta for OH')
plt.plot([float(column.split()[0]) for column in AD_analysis.graph[0][:-1]],[float(column.split()[1]) for column in AD_analysis.graph[0][:-1]])

#AD HH
plt.subplot(132)
plt.xlabel('cos theta')
plt.ylabel('P(cos theta)')
plt.title('PDF cos theta for HH')
plt.plot([float(column.split()[0]) for column in AD_analysis.graph[1][:-1]],[float(column.split()[1]) for column in AD_analysis.graph[1][:-1]])

#AD dip
plt.subplot(133)
plt.xlabel('cos theta')
plt.ylabel('P(cos theta)')
plt.title('PDF cos theta for dipole')
plt.plot([float(column.split()[0]) for column in AD_analysis.graph[2][:-1]],[float(column.split()[1]) for column in AD_analysis.graph[2][:-1]])

plt.show()

where P(cos(theta)) is the angular distribution or angular probabilities.

MeanSquareDisplacement

Analyzing mean square displacement (MSD) MeanSquareDisplacement for water molecules. In this case we are analyzing the average distance that water molecules travels inside protein in XYZ direction (cylindric zone of radius 11[nm], Zmax 4.0[nm] and Zmin -8.0[nm]). A strong rise mean a fast movement of water molecules, a weak rise mean slow movement of particles:

import MDAnalysis
from waterdynamics import MeanSquareDisplacement as MSD

u = MDAnalysis.Universe(pdb, trajectory)
select = "byres name OH2 and cyzone 11.0 4.0 -8.0 protein"
MSD_analysis = MSD(universe, select, 0, 1000, 20)
MSD_analysis.run()
#now we print data ready to graph. The graph
#represents MSD vs t
time = 0
for msd in MSD_analysis.timeseries:
      print("{time} {msd}".format(time=time, msd=msd))
      time += 1

#Plot
plt.xlabel('time')
plt.ylabel('MSD')
plt.title('MSD')
plt.plot(range(0,time),MSD_analysis.timeseries)
plt.show()

SurvivalProbability

Analyzing survival probability (SP) SurvivalProbability of molecules. In this case we are analyzing how long water molecules remain in a sphere of radius 12.3 centered in the geometrical center of resid 42 and 26. A slow decay of SP means a long permanence time of water molecules in the zone, on the other hand, a fast decay means a short permanence time:

import MDAnalysis
from waterdynamics import SurvivalProbability as SP
import matplotlib.pyplot as plt

universe = MDAnalysis.Universe(pdb, trajectory)
select = "byres name OH2 and sphzone 12.3 (resid 42 or resid 26) "
sp = SP(universe, select, verbose=True)
sp.run(start=0, stop=101, tau_max=20)
tau_timeseries = sp.tau_timeseries
sp_timeseries = sp.sp_timeseries

# print in console
for tau, sp in zip(tau_timeseries, sp_timeseries):
      print("{time} {sp}".format(time=tau, sp=sp))

# plot
plt.xlabel('Time')
plt.ylabel('SP')
plt.title('Survival Probability')
plt.plot(tau_timeseries, sp_timeseries)
plt.show()

One should note that the stop keyword as used in the above example has an exclusive behaviour, i.e. here the final frame used will be 100 not 101. This behaviour is aligned with AnalysisBase but currently differs from other waterdynamics classes, which all exhibit inclusive behaviour for their final frame selections.

Another example applies to the situation where you work with many different “residues”. Here we calculate the SP of a potassium ion around each lipid in a membrane and average the results. In this example, if the SP analysis were run without treating each lipid separately, potassium ions may hop from one lipid to another and still be counted as remaining in the specified region. That is, the survival probability of the potassium ion around the entire membrane will be calculated.

Note, for this example, it is advisable to use Universe(in_memory=True) to ensure that the simulation is not being reloaded into memory for each lipid:

import MDAnalysis as mda
from waterdynamics import SurvivalProbability as SP
import numpy as np

u = mda.Universe("md.gro", "md100ns.xtc", in_memory=True)
lipids = u.select_atoms('resname LIPIDS')
joined_sp_timeseries = [[] for _ in range(20)]
for lipid in lipids.residues:
    print("Lipid ID: %d" % lipid.resid)

    select = "resname POTASSIUM and around 3.5 (resid %d and name O13 O14) " % lipid.resid
    sp = SP(u, select, verbose=True)
    sp.run(tau_max=20)

    # Raw SP points for each tau:
    for sps, new_sps in zip(joined_sp_timeseries, sp.sp_timeseries_data):
        sps.extend(new_sps)

# average all SP datapoints
sp_data = [np.mean(sp) for sp in joined_sp_timeseries]

for tau, sp in zip(range(1, tau_max + 1), sp_data):
    print("{time} {sp}".format(time=tau, sp=sp))