online GROMACS Workshop + troubleshooting
GROMACS is a popular open-source molecular dynamics simulation software that can simulate the behaviour of complex molecular systems. GROMACS was initially developed in the early 1990s by researchers at the University of Groningen in the Netherlands, and has since been continuously updated and maintained by a large community of developers throughout the world because of its open-source nature.
GROMACS is well-known for its high performance and efficiency, making it an ideal tool for simulating a wide range of chemical and biochemical systems, including proteins, nucleic acids, lipids, carbohydrates, and polymers. It has a wide range of capabilities, which include energy minimisation, molecular dynamics simulations, and free energy calculations, as well as tools for analysing and visualising simulation results. GROMACS has an easy-to-use interface and a lot of documentation, which makes it an excellent starting point for beginners.
How we conduct this GROMACS workshop
Molecular Dynamics is a complicated art that needs training and practice, as well as a solid theoretical foundation. Also, you may encounter many problems in practice. We know these as a fact. Thus, the Insilicosci GROMACS workshop is more than just an online course.
Our GROMACS workshop has two major components: online content and troubleshooting meetings. The online content includes video tutorials and some assignments. In each session, first we explain the theory behind the computational methods, then we use those methods in practice. At the end, there are a few exercises to solidify your understanding. You can expect an average of 1.5 hours of video in each session. In addition, each session includes a 1-hour troubleshooting meeting during which you can discuss any problems that may have occurred during that session.
Syllabus
Session One: Getting Started with Molecular Dynamics Simulation
- What is Molecular Dynamics Simulation?
- Introduction to Molecular Dynamics Force Fields
- Introduction to Molecular Dynamics Integration Schemes
- Introduction to Molecular Dynamics Ensembles
- Introduction to Periodic Boundary Conditions
- Installing GROMACS and VMD on a Linux Machine
Session Two: A Simple Protein MD Simulation
- Introduction to GROMACS Inputs and Output Files
- GROMACS Simulation Diagram
- Finding and Preparing a Protein Structure
- Preparing the Protein Topology
- Adding Solution and Ions to the System
- Minimising the Molecular System
- Performing MD Simulation in NVT and NPT Ensembles
- Hands-On Practice: Simulating a Human Angiogenin Protein
- Exercise: Simulating a Human Pepsin Protein
Session Three: Protein-Ligand Simulation
- Preparing the Ligand Structure
- Introducing Various Tools for Generating Topology
- Creating the Ligand Topology
- Building the Protein-Ligand Complex
- Mixing Protein and Ligand Topologies
- Adding Solvent and Minimising System
- Equilibrating the Protein-Ligand Complex
- Performing the MD Production Run
- Hands-On Practice: Simulating Urease Inhibition Protein-Ligand Complex
- Exercise: Investigating a New Urease Inhibitor Drug
Session Four: After-Simulation Analyses
- Checking Equilibrium Criteria
- Checking Structural Stability
- Re-centring and Stripping out Molecules after Simulation
- Analysing Compactness of Macro-molecules
- Analysing Structural Deviations
- Analysing Ligand Dynamics
- Analysing Protein-Ligand Interactions
- Calculating Mass Density Profile
- Performing Secondary Structure Analysis by (DSSP)
- Performing Principal Component Analysis (PCA)
- Calculating Components of Binding Energy Using the MM-PBSA Method
- Hands-On Practice: Analysing the Human Angiogenin Protein
- Hands-On Practice: Analysing the Urease Inhibition Protein-Ligand Interaction
Session Five: Looking Deeper into Force Fields
- Explaining Various GROMACS Force-Field Files
- Creating Molecular Structure of Nano-materials
- Immersion of Molecules in a Gaseous Medium
- Creating Topology Template for Non-Standard Molecule and Ligands
- Adding Parameters to Force-Field Files for Non Standard Molecules and Ligands
- Hands-On Practice: Writing Force-Field Parameters from Scratch for a Boron-Nitride Nanotube
- Exercise: Writing Force-Field Parameters from Scratch for a Carbon Nanotube
Session Six: Dealing with Metallic Ligands and Molecules
- Introduction to the Antechamber Software
- Introduction to the MCPB Software
- Installing Antechamber and MCPB on a Linux Machine
- Preparing an Organometallic Ligand Structure
- Computing Missing Parameters Using Gaussian Software
- Combining the Organometallic Ligand and Protein Topologies
- Hands-On Practice: Making Topology for Carboplatin, an Organometallic Anticancer Drug
- Exercise: Making Topology for Auranofin, the Anti-Arthritic Gold-Containing Drug
Session Seven: Using the Umbrella Sampling Method to Calculate Binding Energy
- Introduction to the Umbrella Sampling Method
- Introduction to the Weighted Histogram Analysis Method (WHAM)
- Generating Initial Configurations for the Umbrella Sampling Analysis
- Extracting Suitable Frames from the Trajectory
- Performing Umbrella Sampling on Each Configuration
- Calculating Free Energy of Binding and Potential of Mean Force (PMF) Using the WHAM
- Hands-on Practice: Calculating Binding Free Energy Between the Doxorubicin Drug and β-cyclodextrin
- Exercise: Calculating Binding Free Energy Between the Doxorubicin and 2-hydroxy propyl-β-cyclodextrin,
Session Eight: Bio-membrane Simulation
- Introduction to CHARMM-GUI Web Application
- Designing Gram-Positive and Gram-Negative Bacterial Membranes
- Designing Human Normal-Cell and Cancer-Cell Membranes
- Designing a Peptide-Membrane Complex
- Equilibration and Production Run of the Peptide-Membrane Complex System
- Analysing the Peptide-Membrane Trajectory File
- Hands-on practice: Investigating Interaction Between a Human Antimicrobial Peptide (LL-37) and Gram-Negative Bacterial Membranes
- Practice: Investigating Interaction Between an Antimicrobial Peptide and Gram-Positive Bacterial Membranes
Certification
After finishing the GROMACS workshop, you can apply for certification. The certification does not include a grade and only confirms that you participated in the GROMACS workshop. The certification requirement is that you complete all the sessions and submit at least 80 percent of the assignments correctly.