Author: Dmitriy Marin

Analyzing molecular trajectories with MDAnalysis in SAMSON

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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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Making nano-batarangs (and more)

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Graphene batarang

Have you ever thought about how you could create the Batman’s batarang at the nanoscale? Maybe it won’t fight cancer or viruses, but every scientist, like a hero, needs tools to work on their cause. In this post, we introduce two such tools that can be used for creating nano-batarangs and other complex-shaped objects at the atomic level by selecting atoms and modifying some of their properties using mathematical expressions and scripting language. The Simple Script App allows you to…

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