Plotting Energy Components in Jupyter Notebook

Overview

Teaching: 25 min
Exercises: 0 min

Questions

• How to extract energy components from simulation logs?

• How to load and plot energy components?

Objectives

• Learn to extract energy components from simulation logs

• Learn to plot energy components

Extracting Energy Components from Simulation Logs.

We are now ready to use pytraj in the Jupyter notebook. Let’s plot energies from the simulation logs of our equilibration runs.

First, we load pandas and matplotlib modules. Then move into the directory where the input data files are located:

import pandas as pd
import matplotlib.pyplot as plt

%cd ~/workshop_pytraj/example_01

Extract some energy components (total energy, temperature, pressure, and volume) from the equilibration log and save them in the file energy.dat:

!./extract_energies.sh equilibration_1.log

File extract_energies.sh is shell script calling cpptraj program to do the job:

#!/bin/bash
echo "Usage: extract_energies simulation_log_file" 
log=$1

cpptraj << EOF
readdata $log
writedata energy.dat $log[Etot] $log[TEMP] $log[PRESS] $log[VOLUME] time 0.1
EOF

Plotting energy components

Read the data saved in the file energy.dat into a pandas dataframe and plot it:

df=pd.read_table('energy.dat', delim_whitespace=True)
df.columns=["Time", "Etot", "Temp", "Press", "Volume"]
df.plot(subplots=True, x="Time", xlabel="Time, ps", figsize=(6, 8))
plt.show()

Key Points