Category: Development updates

Normal Modes Advanced

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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

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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 !

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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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New functions for memory management

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Memory management is an important issue in an application such as SAMSON, where developers independently write modules, and users may use these modules in combination – and in any order. Moreover, since users may undo and redo actions, SAMSON has to ensure that any allocated memory is properly freed when it cannot be used anymore. To help developers achieve this, the SAMSON SDK now contains new functions to manage memory. Assume for example a function adds a new structural model…

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Cite your research in SAMSON Elements

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If a SAMSON Element corresponds to one or more research papers, you now have the possibility of letting users know about them. First, add the SBGWindow::Citable tag in the getFormat function of your GUI (for example, the GUI of the app, or the property window of an interaction model): int SEEMyModelProperties::getFormat() const {   return (SBGWindow::Savable | SBGWindow::Lockable | SBGWindow::Citable);   }int SEEMyModelProperties::getFormat() const { return (SBGWindow::Savable | SBGWindow::Lockable | SBGWindow::Citable); } This adds a question mark to the window…

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