GROMACS Wizard

In this tutorial, we will present you GROMACS Wizard Extension, a SAMSON extension for system preparation and simulation both locally and in the Cloud using the well-known GROMACS package.

The GROMACS Wizard Extension integrates the main GROMACS features into SAMSON – it provides the possibilities to easily prepare systems for simulation with GROMACS and run GROMACS simulations locally or in the Cloud, and get the results as simulation trajectories and plots. It is shipped with one of the latest versions of GROMACS (the latest version of the extension ships GROMACS 2021.3) which means that you do not need to compile and install the GROMACS package yourself. But it also gives you the possibility to use your local installation of GROMACS if you wish so.

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

Tutorial content

• • 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
  • Applying custom parameters
  • Launching computations in the Cloud
  • Using custom GROMACS version and performance parameters

Installing GROMACS Wizard

To install the GROMACS Wizard Extension, sign in on the SAMSON Connect website and go to SAMSON Extensions where you can find GROMACS Wizard, or simply open this link: GROMACS Wizard Extension. Once you are signed in, you should be able to add a SAMSON Extension in one click (see User guide: installing SAMSON Extensions if you need help with installing a new SAMSON Extension). On the next launch of SAMSON, the newly added extension will be automatically downloaded and installed for you. If you need help with adding SAMSON itself, please visit the User Guide: Installing SAMSON.

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

1. In the Apps menu of SAMSON
2. In the Interface menu > Preferences > Updates > SAMSON Extensions list in SAMSON
3. Under User > My Extensions when you are signed in at SAMSON Connect