GROMACS Wizard

This tutorial path introduces the GROMACS Wizard Extension, a SAMSON extension for preparing systems and running GROMACS simulations locally or in the cloud.

By the end of this tutorial sequence, you should be able to:

• clean and prepare a system for simulation
• minimize and equilibrate it
• launch a production MD run
• branch into cloud jobs, batch workflows, pulling, umbrella sampling, and related advanced tasks

The GROMACS Wizard Extension integrates the main GROMACS features directly into SAMSON. It ships with a compatible GROMACS build, so you can get started without installing GROMACS separately. If you already have a local GROMACS build that you want to use, GROMACS Wizard can work with that as well.

This extension is available on Windows, Linux, and macOS.

Before you start

• Add GROMACS Wizard Extension.
• If you are new to the workflow, follow the pages below in order.
• The tutorial often uses the 1AKI structure as an example, but you can follow the same workflow with your own system.

Learning path

• Installation
• Pre-processing
• Step 1: Prepare
• Step 2: Energy Minimization
• Step 3: NVT Equilibration
• Step 4: NPT Equilibration
• Step 5: Production Molecular Dynamics Simulation
• Periodic boundary conditions
• Protein-ligand systems
• Applying custom parameters
• Adding custom index groups
• Batch computations
• Coarse-grained systems
• COM pulling
• Umbrella Sampling
• Potential of Mean Force (PMF) analysis
• Launching computations in the Cloud
• Using custom GROMACS version and performance parameters

If you only need one task, such as cloud jobs or custom parameters, you can jump directly to that page after completing the earlier prerequisite steps.

Installing GROMACS Wizard

To install the GROMACS Wizard Extension:

1. Sign in on SAMSON Connect.
2. Open the GROMACS Wizard Extension page.
3. Click Add to add the extension to your account.
4. Restart SAMSON so the extension is downloaded and installed.

If you need help with the platform itself, see User guide: installing SAMSON Extensions and User Guide: Installing SAMSON.

Note: You can check whether you have this SAMSON Extension in at least three different ways:

• In Home > Apps > Biology
• In the Interface > Preferences > Updates > SAMSON Extensions list in SAMSON
• Under User > My Extensions when you are signed in at SAMSON Connect