Author: Dmitriy Marin

GROMACS Wizard – Batch Computations

This section is a part of the GROMACS Wizard tutorial. This tutorial demonstrates how to perform batch computations using GROMACS Wizard for a set of initial conformations of a single molecular system. To use an existing trajectory, load it in SAMSON. You can also create a trajectory or a set of conformation in SAMSON using various tools: editors (Move editors, Twister), various extensions (AutoDock Vina Extended, Normal Modes Analysis, Ligand Path Finder, Protein Path Finder, protein-protein docking with Hex, etc.), animations (Dock,…

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GROMACS Wizard – PMF Analysis

This section is a part of the GROMACS Wizard tutorial. This tutorial demonstrates how to compute the Potential of Mean Force (PMF) using the Weighted Histogram Analysis Method (WHAM) in GROMACS Wizard. Switch to the WHAM Analysis tab in GROMACS Wizard. Choose the project path or click on auto-fill if the previous project you ran was the Umbrella Sampling simulation. The project folder might be a result of the batch computation, and it needs to contain numbered subfolders each containing simulation…

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GROMACS Wizard – COM Pulling

This section is a part of the GROMACS Wizard tutorial. This tutorial demonstrates how to perform COM Pulling using GROMACS Wizard. Reference: We will use the same system, 2BEG, as in the Umbrella Sampling tutorial by Justin A. Lemkul. 1. Loading the system First, load the system: go to Home menu > Fetch and load 2BEG from the RCSB PDB in mmCIF or PDB format. When loading the structure into SAMSON a pop-up might appear with import options depending on the…

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GROMACS Wizard – Umbrella Sampling

This section is a part of the GROMACS Wizard tutorial. This tutorial demonstrates how to perform Umbrella Sampling using GROMACS Wizard. To perform Umbrella Sampling you first need to obtain a set of initial conformations. You can do it in one of the following ways: From GROMACS trajectory obtained from some simulation, e.g. by performing COM pulling simulation. From a set of conformations or a path (trajectory) created outside SAMSON or in SAMSON. Then you need to perform NPT equilibration and…

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GROMACS Wizard – Adding custom index groups

This section is part of the GROMACS Wizard tutorial. GROMACS automatically generates standard index groups for your system based on its structure (e.g., protein, water, ions, etc.). But sometimes you might want to add custom index groups that we later be useful for analysis or during the simulation (e.g., as pull coordinate groups). You can do this thanks to GROMACS Wizard which allows you to use the extensive selection mechanisms available in SAMSON (see User Guide: Selecting). When dealing with…

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Coronavirus: computing the opening motion of the SARS-CoV-2 spike

In this small article, we provide a brief introduction about the way the SARS coronavirus 2 (SARS-CoV-2) operates, and we provide results of our computations of the motion of its spike from its closed state to its open, receptor-binding state. Introduction The SARS coronavirus 2 (SARS-CoV-2) – the virus that causes the COVID-19 disease – has transmembrane spikes (S proteins on the image below) attached to its lipid membrane. It is because of these spikes – their relatively large number –…

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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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