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Molecular Dynamic Simulation

The simplest method to understand molecular dynamics! You will master the fundamentals of molecular dynamics in this course, including

Molecular Dynamics: What is it? The force field is what? , Molecule preparation, energy minimization, system equilibration, molecular dynamics software, Ubuntu installation in Windows, GROMACS installation, GROMACS data format, and trajectory analysis

More theory and applications. A wonderful time! 

Join the course at an affordable price :

Indian Nationals - Rupees 10,000 + GST

Foreign Nationals - $160 (USD)

Key Takeaways from the Internship:

  1. Linux usage

  2. Gromacs installation

  3. System preparation

  4. Energy Minimisation

  5. Equilibration

  6. Analysis

  7. Certificates of Completion 

  8. Video Lectures

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Introduction to Molecular Dynamic Simulation

  • What is Simulation?

  • Linux Installation on Windows

  • Gromacs Installation

Molecular Dynamic Simulation using GROMACS

  • What is GROMACS?

  • Usage of GROMACS

  • Protein Simulation

  • Protein-Ligand simulation

  • Result analysis

  • Assignment/Exercise

Visualisation Software

  • Xmgrace

  • Inkscape

  • GIMP

Theoretical Understanding of Molecular Dynamic Simulation

  • What is Molecular Dynamic Simulation?

  • Different algorithms involved

  • Energy Minimisation

  • Equilibration

  • Theoretical Concept of MD

  • Assignments/Exercise

MD Pipeline

  • MM-PBSA Calculation

  • Dynamic Cross-Correlation Matrix

  • Root Mean Square Deviation (RMSD)

  • Root Mean Square Fluctuation (RMSF)

  • Radius of Gyration (Rg)

  • Hydrogen Bond

  • Solvent Accessible Surface Area (SASA)

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