Export atom trajectories along paths

In this tutorial, we will show how to export atoms positions (for all atoms in the system or for a selection of atoms) along paths in PDB files thanks to the Export Along Paths app. This could be useful for example if you want to generate reaction coordinates for free energy calculations.   Requirements Export Along Paths Extension Before starting the tutorial, please download the 1pv7_ligand_complex_with_paths (~13 MB) which contains files for this tutorial. Tutorial Launch SAMSON. Load 1pv7_ligand_complex_with_paths.sam file…

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Optimize transition paths with the Parallel Nudged Elastic Band (P-NEB) method

The Nudged Elastic Band (NEB) method allows for finding saddle points and minimum energy paths between known conformations. The method optimizes a number of intermediate images along the path by finding the lowest possible energy for each image while maintaining equal spacing between neighboring images. This constrained optimization is done by adding spring forces. The NEB method can be used, for example, to determine transition paths between already obtained structures corresponding to local energy minima (obtained using, e.g., the FIRE…

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Protein Path Finder

In this post, we will show how to use the Protein Path Finder app for finding possible paths between two conformations of a protein. Content Requirements Tutorial Loading the input model Launching the Protein Path Finder app Setting up the interaction model and the state updater for energy evaluation Setting up the system Defining the sampling box Defining the parameters Running, pausing, or stopping the planner Results Next steps Creating pathlines Improving paths with P-NEB Exporting atoms trajectories along paths…

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Ligand Path Finder

In this post, we will show how to use the Ligand Path Finder app for finding possible ligand unbinding pathways from a protein. Content Requirements Tutorial Loading the input model Launching the Ligand Path Finder app Setting up the interaction model and the state updater for energy evaluation Setting up the system Defining the sampling box Defining the parameters Running, pausing, or stopping the planner Results Next steps Creating pathlines Improving paths with P-NEB Exporting atoms trajectories along paths Requirements…

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Pathlines: show a path of the center of mass of an atomic system

In this post, we will show you how to create pathlines thanks to the Pathlines visual model. Pathlines are visual models which represent the trajectory of the center of mass of selected atoms along selected Paths. Pathlines may be used to understand the motion of a single atom, or a group of atoms, along a path/trajectory. Before starting the tutorial, please, download this archive: Pathlines (~13MB). It contains a file (1pv7_ligand_complex_with_paths.sam) from the Ligand Path Finder tutorial with already computed…

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Making nano-batarangs (and more)

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. Content Simple Script Extension Atoms Selector Extension…

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