Molecular Dynamics Simulation Course

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About 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.

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What Will You Learn?

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

Course Content

Molecular Dynamics Simulations: GROMACS

  • Getting Started With Molecular Dynamics Simulation – Pre-processing of Protein Structure and Removal of Unnecessary Structural Features
  • pdb2gmx – Construction of Topology File for Simulation
  • Defining a Solvant Box for Simulation
  • Solvation – Adding Water Molecules in Solvant Box
  • Generating Input Run File Replacement of Water Molecules With Ions
  • Genion – Replacement of Water Molecules With Ions
  • Energy Minimization – Relaxing and Fixing the Structure for Simulation
  • GRACE – Visualization and Analysis of Minimized Structure
  • Draft LessonEquibiliration of Protein Structure NVT ENSEMBLE Phase 1
  • Equibiliration of Protein Structure NPT ENSEMBLE Phase 2
  • mdrun – Executing Simulation Analysis

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