Tutorials

Please find below all of the tutorials that should help you learn how to use BioSimSpace.

Reading and writing molecular systems

BioSimSpace has support for reading and writing a large number of common molecular file formats. Unlike many other molecular parsers, BioSimSpace does not attempt to infer the format from the file extension. Instead, it reads the files in parallel using its blazing fast suite of parsers in order to automatically determine the correct format. To...

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Running molecular dynamics

BioSimSpace makes it easy to get up and running with molecular dynamics simulation. Any simulation takes two ingredients: A molecular system This is the set of atoms and molecules that define your system of interest. A simulation protocol This defines what you want to do to the system. You should think of a molecular simulation...

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Configuring a simulation process

In running molecular dynamics we saw how easy it was to set up and run molecular simulations using BioSimSpace. While in most cases the default options are perfectly satisfactory, on occasion you may wish to customise the process to your specific needs. In addition to its high-level interface, BioSimSpace also provides functionality for low-level configuration,...

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Interactive molecular dynamics

When running BioSimSpace interactively, e.g. in a Jupyter notebook, processes are run in the background allowing you to continue with your work, uninterrupted. At any time, it is possible to query the running process for information. (Here we assume that you have initalised a BioSimspace process, see here for details.) To see whether the process...

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Plotting time-series data

BioSimSpace provides several tools that provide additional functionality when working interactively. One of these is the plot function that enables graphing of time series data. This is simply a wrapper around Matplotlib to quickly produce nicely formatted graphs for inclusion in a Jupyter notebook. (Here we assume that you have initalised a BioSimspace process, see...

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Interactive molecular visualisation

Another useful interactive tool provided by BioSimSpace is the View class. This is a wrapper around the excellent NGLView to allow easy visualisation of molecular systems. When creating a View object you can either directly pass a molecular system, or alternatively pass a Process object to allow you to dynamically visualise the latest molecular system...

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Analysing molecular trajectories

BioSimSpace provides functionality for reading, writing, and analysing a variety of common molecular trajectory formats. For example, to load an AMBER NetCDF trajectory from file: import BioSimSpace as BSS traj = BSS.Trajectory(trajectory="traj.nc", topology="topology.prm7") While useful, it is more likely that you will want to create a trajectory from a BioSimSpace process. # Load a molecular...

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