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Biomolecular simulation: Difference between revisions
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add Python packages relevant to BioMolSim
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* [http://www.plumed-code.org PLUMED], a library for code development related to the calculation of free energy in molecular dynamics simulations. See also [[GROMACS]]. | * [http://www.plumed-code.org PLUMED], a library for code development related to the calculation of free energy in molecular dynamics simulations. See also [[GROMACS]]. | ||
* [https://www.rosettacommons.org Rosetta] | * [https://www.rosettacommons.org Rosetta] | ||
=== Python Packages (Python Wheels) === | |||
Our [[Available_Python_wheels|Wheelhouse]] contains a number of Python Wheels that can be installed within a [[Python#Creating_and_using_a_virtual_environment|virtual Python environment]] and are useful in the domain of Biomolecular Simulation. | |||
This list contains a selection of useful wheels, but is not to be considered complete: | |||
* [https://www.mdanalysis.org/ MDAnalysis] is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. | |||
* [http://mdtraj.org/ MDTraj] can also read, write and analyze MD trajectories with only a few lines of Python code with wide MD format support. | |||
* [https://biopython.org/ Biopython] is a set of freely available tools for biological computation. | |||
* [https://foyer.mosdef.org/ foyer] is a package for atom-typing as well as applying and disseminating force fields. | |||
* [https://mbuild.mosdef.org/ mBuild] is a hierarchical, component based molecule builder. | |||
* [https://mdsynthesis.readthedocs.io/ mdsynthesis] is a persistence engine for molecular dynamics data. | |||
* [http://nglviewer.org/ nglview]: NGL Viewer is a collection of tools for web-based molecular graphics. | |||
* [http://parmed.github.io/ParmEd/ ParmEd] is a general tool for aiding in investigations of biomolecular systems using popular molecular simulation packages. | |||
* [http://www.pyretis.org/ PyRETIS] is a Python library for rare event molecular simulations with emphasis on methods based on transition interface sampling and replica exchange transition interface sampling. | |||
Please check the [[Available_Python_wheels|list of available wheels]] and use the [[Python#Listing_available_wheels|avail_wheels command]] on our clusters | |||
to see what is installed. | |||
If you require additional Python packages or newer versions, please [[Technical_support|contact Support]]. | |||
== Benchmarking MD-Simulations == <!--T:8--> | == Benchmarking MD-Simulations == <!--T:8--> | ||