Online GROMACS Workshop

GROMACS is a popular open-source molecular dynamics simulation software that can simulate the behaviour of complex molecular systems. GROMACS is well-known for its high performance and efficiency, making it an ideal tool for simulating various chemical and biochemical systems.

This workshop will teach you how to conduct molecular dynamics simulations on various systems and perform insightful analyses.
This workshop is suitable for those unfamiliar with molecular dynamics and the GROMACS software. All calculations will be taught from the beginning, along with the necessary theoretical background. However, experienced GROMACS users will also find many valuable topics in this workshop.

How the workshop will be conducted

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 this 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 sessions. The online content includes video tutorials and some assignments. In each session, we first explain the theory behind the computational methods, and 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 one hour of video in each session. In addition, each session includes a four-day troubleshooting meeting during which you can discuss any problems that may have occurred during that session. Each session also has assignments to solidify your learning. By submitting %65 of them correctly, you will receive a certification.

The GROMACS workshop is scheduled to take place from July 22 to August 17, 2025.
Registration is open now.
The workshop has limited capacity, and priority will be given to those who complete their enrollment first.

Schedule

The GROMACS workshop is scheduled to take place from July 22 to August 18, 2025.

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 Linux
Installing GROMACS and VMD on Windows

Session Two: A Simple Protein MD Simulation

How to Find and Download Protein Structures
Introduction to the PDB File Format
Visualising a Protein Structure Using VMD
Removing Water Molecules and Fixing Missing Atoms in PDB Files
Overview of the GROMACS Input Workflow
Creating a Topology File for a Protein Structure
Understanding GROMACS Topology (.top) and Coordinate Files
Setting Up a Periodic Boundary Condition (PBC) Box
Adding Solvent Molecules and Ions to the Simulation Box
Energy Minimisation of the Molecular System
Equilibrating the System in the NVT Ensemble
Introduction to Position Restraints in GROMACS
Understanding the GROMACS MDP (Molecular Dynamics Parameters) File
How to Check If the System Has Reached Equilibrium
Equilibrating the System in the NPT Ensemble
Running the Production Simulation
Understanding GROMACS Output Files
Restarting and Extending a Simulation
Visualising and Inspecting Trajectory Files Using VMD
Performing Basic Analysis of Simulation Results
Performing and Interpreting RMSD (Root Mean Square Deviation) Analysis
Performing and Interpreting Radius of Gyration Analysis

Session Three: A Protein-Ligand Simulation

Common Challenges in Protein–Ligand Complex Simulations
Installing and Introducing the pdbfixer Tool
Introduction to the CGenFF Force Field Generator
Preparing a Ligand Structure for CGenFF
Interpreting CGenFF Penalty Scores
Generating GROMACS Topology Files from CGenFF
Running a Test Simulation to Validate Ligand Topology
Generating Protein Topology Using the CHARMM36 Force Field
Combining Protein and Ligand Topology Files
Converting GROMACS Topology Files to .itp Format
Troubleshooting Common Errors in Protein–Ligand Simulations
Creating a New Index Group Using gmx make_ndx
Generating Position Restraints for the Ligand
Analysing Protein–Ligand System Stability Using RMSD
Introduction to Principal Component Analysis (PCA)
Performing PCA on a Protein–Ligand Complex
Plotting and Interpreting the Free Energy Landscape

Session Four: Dealing with Metallic Ligands and Molecules

Introduction to AmberTools and the MCPB.py Workflow
Installing AmberTools24 via Miniconda
Preparing a Protein Structure for Use with MCPB.py
Rebuilding a Ligand Structure for MCPB.py Compatibility
Preparing a Metal Ion for MCPB.py Processing
Performing DFT Calculations to Derive Missing Parameters
Generating Topology and Coordinate Files Using the tLeap Program
Converting AMBER Topology and Coordinate Files to GROMACS Format Using the Acpype Tool
Running a Test Simulation in GROMACS to Validate Setup

Session Five: Bio-Membrane Simulations

Introduction to the CHARMM-GUI Web Application
Building a Simple Lipid Membrane System
Conducting a Membrane System Simulation Using GROMACS
Constructing an Asymmetrical Bilayer Containing Glycolipids
Building a Membrane with a GPI-Anchored Protein
Constructing a Membrane Containing a G-Protein-Coupled Receptor (GPCR)

Session Six: Calculating Free Energy

Introduction to Alchemical Methods for Calculating Free Energy
Overview of Geometrical Methods for Free Energy Calculation
Explaining End-State Methods for Free Energy Calculation
Introduction to the MM-PBSA Method for Free Energy Estimation
Installing the gmx_mmpbsa Program
Calculating Protein–Ligand Binding Energy Using the MM-PBSA Method
Introduction to Free Energy Perturbation (FEP) Methods
Calculating Protein–Ligand Binding Energy Using the FEP Method

Session Seven: PMF and Umbrella Sampling Method

Calculating the Free Energy of Membrane Permeation
Introduction to PMF (Potential of Mean Force) and Umbrella Sampling Methods
Explaining the WHAM (Weighted Histogram Analysis Method)
Preparing the Bilayer System for Umbrella Sampling
Generating the Reaction Coordinate for the Simulation
Extracting Suitable Frames from Trajectories
Running Umbrella Sampling Simulations
Calculating PMF and Free Energy Difference Using WHAM

How to enrol in the workshop

Contacts

WhatsApp number: +44-7943-74-6543

Email: [email protected]

Pricing

Students and Postdocs

Others

129.00 USD

199.00 USD

To use the student & postdoc plan, You need to provide us with a valid student ID card or any document that proves your student or postdoctoral status.
Also, depending on your location, you may qualify for regional discounts. Check the regional discounts section to see how much you can save.

Regional Discounts

We are not communists, but we believe everyone should have the opportunity to learn and thrive, so we offer discounts based on purchasing power in various countries to make education accessible.

To receive a discount for a specific country, you need to be a resident of that country.
If you enrolled with a discount code, do not use a foreign VPS/VPN while participating in the workshops.
To receive a discount code, please send us an image of your student card or any document showing you are currently studying or residing in a specific country.
There is no need for an explanation. Just send your document via WhatsApp or email and introduce yourself.

Please refer to the list below to check how much discount you can receive.

The GROMACS workshop is scheduled to take place from July 22 to August 17, 2025.
Registration is open now.
The workshop has limited capacity, and priority will be given to those who complete their enrollment first.

Sample Video

Watch the sample video on YouTube.
https://youtu.be/-S1eP-iWE8c

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.