Software category listing | Beckstein Lab

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GromacsWrapper

GromacsWrapper

GromacsWrapper is a python package that allows one to call the standard Gromacs tools in Python scripts. It is object-oriented and encourages code reuse and is therefore suitable for scripting complex work flows for setting up or analyzing Gromacs MD simulations.

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MDAnalysis

MDAnalysis

MDAnalysis is an open source, versatile, object-oriented Python library for analyzing molecular dynamics trajectories. It makes it easy to access trajectory data from Python code by interfacing trajectory readers (and writers) with NumPy arrays and to select atoms via a expressive selection syntax. The CHARMM/NAMD, Amber, Gromacs trajectory formats are all supported as well as PDB, GRO, CRD, PQR, and a range of others.

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Our software on GitHub and elsewhere

Our software on GitHub and elsewhere

Most of the code that we are writing and using is accessible through the lab web pages. However, there are odds and ends and small pieces of code that barely justify a web page of their own. Typically, such code can be found in the Becksteinlab GitHub repository

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