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GROMACS

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A molecular dynamics software for simulating proteins, lipids, and nucleic acids, optimized for performance on CPUs and GPUs.

GROMACS
GROMACS

GROMACS (GROningen MAchine for Chemical Simulations) is a highly versatile software used primarily for molecular dynamics (MD) simulations of biomolecules like proteins, lipids, and nucleic acids. Originally developed at the University of Groningen, GROMACS is now maintained by a wide international community and is widely recognized for its exceptional speed and efficiency, making it one of the fastest MD programs available.

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.
  • 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.

Specialized Techniques

  • Umbrella Sampling: For enhanced systematic sampling in computational physics and chemistry.
  • 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.
  • Steered Molecular Dynamics (SMD): Induces changes in biomolecules.
  • Building Biphasic Systems: Constructs complex systems, including lipid bilayers.

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!).

Tip: 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.

Here you can watch our video tutorial too: