GROMACS

Introduction to GROMACS

GROMACS, a project originating in 1991 at the University of Groningen, is a versatile, high-performance software for molecular dynamics. Renowned for efficiently simulating biomolecules such as proteins, lipids, and nucleic acids, GROMACS is an indispensable tool in fields like biophysics, pharmacology, and biochemistry. Explore its history and development and GROMACS GitHub

Key Features of GROMACS

• Efficient Dynamics Simulation: Excelling in simulations for systems ranging from hundreds to millions of particles.
• Diverse Applications: Ideal for studying properties of biomolecules. Learn more.
• Multiple Force Fields: Compatible with AMBER, CHARMM, GROMOS, OPLS, etc. Force Fields Guide.
• Advanced Modeling Techniques: Supports Martini coarse-grained models and GBSA-based implicit solvent models. Martini Model Information.
• Hybrid Dynamics: Facilitates QM/MM hybrid dynamics. QM/MM Hybrid Techniques.

Specialized Techniques

• Umbrella Sampling: For enhanced systematic sampling in computational physics and chemistry. Umbrella Sampling Guide.
• Free Energy Calculations: Involves solvation/hydration and binding free energies. Free Energy Tutorial.
• Replica Exchange Molecular Dynamics (REMD): Addresses local minima in traditional MD simulations. REMD Explained.
• Steered Molecular Dynamics (SMD): Induces changes in biomolecules. SMD Techniques.
• Building Biphasic Systems: Constructs complex systems, including lipid bilayers. Biphasic Systems Tutorial.

How to Run GROMACS:

This example demonstrates how to run a molecular dynamics simulation using GROMACS. We utilize an example provided on GitHub, from which you'll need to download the zip file automated-lysozyme-water-forcefields-GROMACS-master.zip. Additionally, you should create (or download) the run_script.sh file that prepares and runs the simulation inputs.

Steps to Execute on Our Platform

1. Upload Files: Click on the folder icon next to the Volume line and upload both automated-lysozyme-water-forcefields-GROMACS-master.zip and run_script.sh to the working directory (/data) of your project.
2. Set Project Directory: Make sure the Project Directory is set to /data (or the mounted volume to entered!).
   1. if you want to change the Project Directory, make sure to apply the changes in the run_script.sh accordingly.
3. Configure Run Script: In the Run Script field, enter run_script.sh as the input.
4. Create the Project: Click on Create to prepare your project environment.
5. Run the Container: Go to the project tab and start the container to run the script.

Following these steps will begin the GROMACS simulation process, allowing you to analyze the dynamics of the lysozyme in water using the provided example.