Author: Dmitriy Marin

This section is part of the GROMACS Wizard tutorial. GROMACS Wizard allows you to launch GROMACS computations for NVT Equilibration, NPT Equilibration, Production Molecular Dynamics Simulation steps in the Cloud in just a few clicks. In this section, you will learn how to launch GROMACS computations in the Cloud from GROMACS Wizard on an example of the NVT Equilibration step. This procedure is the same for NPT Equilibration and Production Molecular Dynamics Simulation steps. Prerequisites Before going further, please first read…

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This section is a part of the GROMACS Wizard tutorial. For each of the Energy Minimization, NVT Equilibration, NPT Equilibration, and Production Molecular Dynamics Simulation steps you can provide custom molecular dynamics parameters (MDP) using the graphical user interface or by loading them from an existing GROMACS molecular dynamics parameter file (an .mdp file). These parameters are populated with their default values. You can see some of the parameters directly in the tabs and the other parameters can be accessed…

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This section is a part of the GROMACS Wizard tutorial. Using a custom GROMACS version GROMACS Wizard comes with one of the latest versions of GROMACS. But it also provides you with the possibility to use your own version of GROMACS for local computations. This might be useful if you would like to use the GROMACS package installed on your system or use a specific GROMACS version for reproducibility reasons. To use a locally installed version of GROMACS, press the Settings…

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This section is part of the GROMACS Wizard tutorial. Once the equilibration of the system is completed – the system’s temperature and density have stabilized at the desired values – we can finally run a production molecular dynamics (MD) simulation. Switch to the Simulate tab. Selecting input structure When launching the NPT Equilibration step, GROMACS Wizard requires you to provide one of the following: The path to a GRO file resulting from the previous step: either a GRO file resulting from…

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This section is part of the GROMACS Wizard tutorial. Once the system has been successfully minimized and the system’s temperature has stabilized at the desired value, it is necessary to apply pressure to the system until it reaches the correct density. This second equilibration phase is aimed at stabilizing the system’s density at the desired value by performing equilibration using the NPT ensemble (constant Number of particles, Pressure, and Temperature) also known as “isothermal-isobaric”. Switch to the Equilibrate (NPT) tab. Selecting input…

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This section is part of the GROMACS Wizard tutorial. Once the system has been successfully minimized, it is necessary to Equilibrate the system to bring it to the desired temperature and pressure/density and stabilize it. Equilibration is often conducted in two phases. The first one is aimed at bringing the system to the desired temperature (the one that you would like to simulate) and stabilizing it by performing equilibration using the NVT ensemble (constant Number of particles, Volume, and Temperature)…

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This section is part of the GROMACS Wizard tutorial. Once the system has been preprocessed and validated, we can start the preparation step. To launch GROMACS simulations, we first need to prepare the system: Choose the model (force field and solvent). Choose the molecular system and, optionally, choose a set of conformations or a path for a batch project. Define the periodic box. Choose what and how many ions should be added. Run preparation During the preparation step, GROMACS Wizard…

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This section is part of the GROMACS Wizard tutorial. Once a system or a batch project has been successfully prepared, it is necessary to perform the Energy Minimization (EM) step to ensure that the system has no steric clashes or inappropriate geometry. Switch to the Minimize tab. Selecting input structure When launching the Energy Minimization step, GROMACS Wizard requires you to provide one of the following: The path to a GRO file resulting from the previous step: either a GRO…

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This section is a part of the GROMACS Wizard tutorial. Load the system In this tutorial, we will be using the 1AKI structure. You can download it from the RCSB Protein Data Bank website by clicking on Home > Fetch. Enter the PDB code 1AKI (you can select any format: PDB, PDBx/mmCIF, or MMTF), and click Load. Depending on the format, a pop-up dialog will appear asking about import parameters – you can leave them to their default values. If you…

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This tutorial presents the GROMACS Wizard Extension, a SAMSON extension for system preparation and simulation 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, run GROMACS simulations locally or in the Cloud, and get the results as simulation trajectories and plots. It ships GROMACS (the latest version of the extension ships GROMACS 2021.3) meaning that…

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