Analyzing molecular trajectories with MDAnalysis in SAMSON

MDAnalysis is a well-known Python library for analyzing molecular dynamics trajectories. In this tutorial, we demonstrate how it can be used to analyze trajectories saved in Path nodes in SAMSON and superimpose structures. Analyzing trajectories Let us, for example, compute the radius of gyration and the RMSD for a protein with trajectories saved in Path in SAMSON. To use the functionality of MDAnalysis, we need to export trajectories we would like to analyze from SAMSON into a format supported by…

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RDKit – SMILES Manager

Hello everyone, In this post I will present you the new version of the RDKit-SMILES Manager module that I integrated in the SAMSON platform. As some of you know, RDKit is an open source toolkit for cheminformatics which is widely used in the bioinformatics research. One of its features is the conversion of molecules SMILES strings to a 2D and 3D structures. The module interface presents two tabulations: Manage SMILES and Replace fragments. I will present these two sections one by one…

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Building nanotubes models with SAMSON

In this quick tutorial, you will learn how to easily generate nanotube models within SAMSON. Nanotube creator First, make sure you have the Nanotube creator SAMSON Element that you can find on SAMSON Connect: If you need help with installing new SAMSON Elements to your SAMSON installation, please visit this page. If you need help with installing SAMSON itself, please visit this page. Note: you can check whether you have this SAMSON Element in at least three different ways: In…

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SAMSON 0.7.0 is available on Windows, Linux and Mac!

We are proud to announce that SAMSON 0.7.0 is now available on Windows, Linux and Mac! SAMSON 0.7.0 has tons of new features and improvements, both in its core and through SAMSON Elements, so here’s an overview. Python scripting Here it is: Python scripting is now available! Most of the SAMSON API is exposed in Python, and a Jupyter console embedded in SAMSON allows you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from…

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Normal Modes Advanced

Hello all, Welcome to this tutorial, I will present you the functionalities of the Normal Modes Advanced (NMA) SAMSON Element. This SAMSON Element computes the nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134, DOI: 10.1021 / acs.jctc.7b00197.). First, you have to import a structure. For this tutorial I used the 1vpk PDB entry. Then, you launch the NMAL module…

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What’s coming up next

As SAMSON 0.7.0 is approaching, we would like to highlight a few upcoming features that we feel are bringing us a little closer to our vision of a federating platform for computational nanoscience. Python scripting Python scripting is coming to SAMSON 0.7.0, and we are (very) excited about it. Most of the SAMSON API is now exposed in Python, and this will allow you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from scripts.…

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Ready, Set… FIRE !

Geometry optimization is a fundamental step in many molecular modeling applications, used to produce stable, realistic structures which correspond to energy minima. Many algorithms have been developed for energy minimization, and we have just released a new SAMSON Element that implements the FIRE minimizer described by Bitzek et al.: Erik Bitzek, Pekka Koskinen, Franz Gähler, Michael Moseler, and Peter Gumbsch Structural Relaxation Made Simple Physical Review Letters, Vol. 97, 170201 (2006) FIRE, which stands for Fast Inertial Relaxation Engine, is…

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Sixteen step-by-step tutorials from SAMSON School 2017

SAMSON School 2017 is now over, and this year sixteen lectures had accompanying written step-by-step tutorials! Feel free to follow the links below to learn how to install and use SAMSON, as well as develop your own SAMSON Elements and share them on SAMSON Connect: Users program Installing SAMSON We introduce the Users program of the SAMSON School and SAMSON, the software platform for computational nanoscience. We highlight the need for an integrated platform able to combine diverse domains of…

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