Resources 4 | 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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Lipidbook

Lipidbook

Lipidbook is a public repository and database for force field parameters with a special emphasis on lipids, detergents, and similar molecules that are of interest when simulating biological membranes.

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