Molecular Dynamics Simulation Course


About This Course

Molecular Dynamics Simulation Course Allows You To Develop The Advanced Level Skills In Analyzing MD Simulations

Molecular Dynamics is a computer simulation approach permitting the time evolution prediction of an interacting particular system which involves the generation of atomic trajectories of a system using numerical integration of Newton’s laws of motion to define specific interatomic potential using the initial condition and boundary condition.

It is one of the principle approaches for the study of biological molecules computationally for calculating the time dependent behavior of a molecular system. It provides detailed information about the fluctuations and conformational changes in proteins and nucleic acids.

MD simulation analysis is one of the essential steps while designing novel drugs using computational approaches. MD analysis not just evaluates and validates the protein structures, either predicted computationally or experimentally, but also validates the drug-target compatibility by providing various statistical information about the interacting drug-target complex.

In this course you’ll learn how to develop expertise in molecular dynamics simulations to predict the most suitable in silico conformations of biological macromolecules for drug designing & development and find the protein-protein interaction networks.

Joining and learning from the Molecular Dynamics Simulation Course can enhance your biological career by learning through various useful & informative pre-recorded lectures on Molecular Dynamics Simulation analysis using GROMACS.

Learning Objectives

Protein Structure Preparation
Energy Minimization
Minimized Structure Visualization
NVT Ensemble
NPT Ensemble
Simulation Execution

Target Audience

  • The target audience for the Basic Linux Scripting For Bioinformatics are biologists, beginner or intermediate Bioinformaticians or data analysts with no or little experience in applications of computational bioinformatics and analysis.
  • However, a superficial understanding of molecular biology and logic development for coding is expected from you before you join the course.
  • Bioinformatics is quite easy to get started in, even if you lack a proper understanding of the underlying concepts of Bioinformatics databases, servers, tools and the algorithms working behind them.


11 Lessons1h 20m

Molecular Dynamics Simulations: GROMACS

Getting Started With Molecular Dynamics Simulation – Pre-processing of Protein Structure and Removal of Unnecessary Structural Features12:34
pdb2gmx – Construction of Topology File for Simulation9:01
Defining a Solvant Box for Simulation00:04:14
Solvation – Adding Water Molecules in Solvant Box00:05:31
Generating Input Run File Replacement of Water Molecules With Ions00:06:55
Genion – Replacement of Water Molecules With Ions00:04:19
Energy Minimization – Relaxing and Fixing the Structure for Simulation00:11:25
GRACE – Visualization and Analysis of Minimized Structure00:04:12
Equibiliration of Protein Structure NVT ENSEMBLE Phase 100:08:38
Equibiliration of Protein Structure NPT ENSEMBLE Phase 200:08:10
mdrun – Executing Simulation Analysis00:03:47


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30% off
All Levels
Duration 1.3 hour
11 lectures

Material Includes

  • Step-by-step pre-recorded lectures
  • Learn any time, any where!
  • Transcription
  • Notes
  • Coding scripts
  • BioPresentations
  • Exercises
  • Automated Evaluations (MCQs)
  • 100% Authentic Certificate

Enrolment validity: 30 days

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