Create molecular boxes with Molecular Box Builder

Molecular Box Builder makes it possible to construct systems by inserting molecules in a box or filling a box with molecules. The Molecular Box Builder app can be found in the App menu > Assembly or via the “Find everything” (Shift+E) in the top-right corner of SAMSON. Setting a molecule Select a system with which you would like to populate a box in the Document view or in the Viewport. The system can be a single molecule or a set of molecules…

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Construct polymers with Polymer Builder

Polymer Builder makes it possible to construct polymers out of various building blocks: individual monomers and sequences of monomers. The Polymer Builder app can be found in the App menu > Assembly or via the “Find everything” (Shift+E) in the top-right corner of SAMSON. Registering new monomers In the Document view or in the Viewport, select a monomer that you would like to add. Click on the “Register monomer from selection” button to add a new monomer based on the…

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GROMACS Wizard – Periodic boundary conditions

“GROMACS uses periodic boundary conditions, combined with the minimum image convention: only one – the nearest – image of each particle is considered for short-range non-bonded interaction terms. For long-range electrostatic interactions this is not always accurate enough, and GROMACS therefore also incorporates lattice sum methods such as Ewald Sum, PME and PPPM.” (GROMACS Manual: Periodic boundary conditions) GROMACS Wizard supports the following shapes for space-filling unit cells: Cubic, Orthorhombic, Triclinic, Rhombic dodecahedron, Truncated octahedron. You can choose which unit…

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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,…

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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…

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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,…

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GROMACS Wizard – Using custom GROMACS version and performance parameters

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…

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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…

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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,…

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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)…

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