Building molecules with SAMSON

In this tutorial, you will learn how to build molecules in SAMSON from atoms and fragments. You can find an introduction to the building functionality in What’s new in SAMSON 2020. We recommend going through the interactive tutorials integrated into SAMSON (Help menu > Tutorials) that will guide you through the basic operations. Specifically, we recommend going through the following interactive tutorials: Working with documents Selecting in the Viewport Building with atoms Moving objects in the Viewport In this tutorial,…

More…

GROMACS Wizard – Computing in the cloud

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…

More…

GROMACS Wizard – Applying custom parameters

This section is a part of the GROMACS Wizard tutorial. For each of the Energy Minimization, NVT Equilibration, NPT Equilibration, Production Molecular Dynamics Simulation steps you can provide custom molecular dynamics parameters using the graphical user interface or by loading them from an existing GROMACS molecular dynamics parameter file (an .mdp file). By default, these parameters are populated with their default values. To inspect or modify them, click the All… button present in each of the aforementioned tabs (steps). Once clicked,…

More…

GROMACS Wizard – Using custom GROMACS version

This section is a part of the GROMACS Wizard tutorial. GROMACS Wizard comes with the latest version 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 button () at the top of…

More…

GROMACS Wizard – Step 5: Production Molecular Dynamics Simulation

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 Production MD step, GROMACS Wizard requires you to provide a path to a GRO file resulting from the previous step: either a GRO file resulting from the NPT Equilibration…

More…

GROMACS Wizard – Step 4: NPT Equilibration

This section is part of the GROMACS Wizard tutorial. Once 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 structure When launching the NPT Equilibration step,…

More…

GROMACS Wizard – Step 3: NVT Equilibration

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)…

More…

GROMACS Wizard – Step 1: Prepare

This section is part of the GROMACS Wizard tutorial. Once the system has been preprocessed and validated we can start the preparation step. In order to launch GROMACS simulations, we first need to prepare the system: choose the model (force field, solvent, ions), define the box. During the preparation step, GROMACS Wizard will generate a model, and add solvent and ions if necessary. Choosing the results folder First, let’s choose a folder where we would like the results to be…

More…

GROMACS Wizard – Step 2: Energy Minimization

This section is part of the GROMACS Wizard tutorial. Once the system 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. Content Selecting input structure Choosing parameters Run energy minimization Importing the results Plots Checking results Selecting input structure When launching the Energy Minimization step, GROMACS Wizard requires you to provide a path to a GRO file resulting…

More…

GROMACS Wizard – Pre-processing of the system

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 or you can easily get it using the Protein Data Bank Downloader Extension (you can add this free extension from the SAMSON Connect). Open this extension via Apps menu > Biology > Download from Protein Data Bank or simply search for it in the Find commands…

More…