Molecular Dynamics Using Python: Analysis with MDAnalysis Library

Molecular Dynamics Using Python

Introduction
Molecular Dynamics is a method or technique which is a subject of simulation for the study
related to physical movement of atom and more precisely particles.Those particles are interacted
freely with others while wandering. At that interaction, a force is exerted among the particles and
potential energies of them are being calculated by interatomic barrier (McGibbon et al., 2015,
pp.1528-1532). In this case the orbital path of molecules are determined by solving the
Newtonian equations of motion numerically (Mou et al., 2015, pp.2697-2706).

MDAnalysis Library:
The analysis of Molecular Dynamics is done using Python with help and implementation of
MDAnalysis library. This specific library is used to analyze the trajectories of Molecular
Dynamics simulation in many different formats. It has the capability to choose atom suitably for
analysis and visualization (Gowers et al., 2016, pp. 98-105).
Installation Guide for MDAnalysis:
In a recent work, Jupyter Notebook via Anaconda Navigator is used for quick simulation. The
updated version of this library can be installed in Anaconda cloud or by “conda” installation with
the following query (Rajendiran and Durrant, 2018, pp.748-755).
condaconfig --add channels conda-forge
conda update --yes conda
MDAnalysis support both Python3.x and Python2.x. For this installation the environment should
be created as follows:
conda create --yes -n mdaenvpython=3.6
Finally, after creating the environment, the following code test the environment:
conda install --yes -n mdaenvMDAnalysisMDAnalysisTests
At the next step, the environment will be activated:
source activate mdaenv
New Approach: