wiki.biowerkzeug.org

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This Wiki discusses biomolecular simulations with Hippo. And other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the forums. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better change it. If you have useful tips and tricks share them with everyone else. If you have comments on any article in this Wiki start a discussion on the discussion. When you edit pages. See Help→Editing.

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This Wiki discusses biomolecular simulations with Hippo. And other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the forums. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better change it. If you have useful tips and tricks share them with everyone else. If you have comments on any article in this Wiki start a discussion on the discussion. When you edit pages. See Help→Editing.

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5 not this hippo

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9 analysis

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Main Page - Biowerkzeug Wiki | wiki.biowerkzeug.org Reviews

https://wiki.biowerkzeug.org

This Wiki discusses biomolecular simulations with Hippo. And other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the forums. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better change it. If you have useful tips and tricks share them with everyone else. If you have comments on any article in this Wiki start a discussion on the discussion. When you edit pages. See Help→Editing.

INTERNAL PAGES

wiki.biowerkzeug.org

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Download - Biowerkzeug Wiki

http://wiki.biowerkzeug.org/index.php/Download

Binaries are publicly available from the Biowerkzeug.com download page. Note that by downloading you consent to the the license. Is trivial because the program comes as a precompiled executable and only requires a few additional data files. Retrieved from " http:/ wiki.biowerkzeug.org/index.php/Download. This page was last modified on 17 November 2008, at 16:49. This page has been accessed 8,513 times.

2

Molecular dynamics - Biowerkzeug Wiki

http://wiki.biowerkzeug.org/index.php/Molecular_dynamics

Simulating the motion of molecules by iteratively solving Newton's equations of motion. Retrieved from " http:/ wiki.biowerkzeug.org/index.php/Molecular dynamics. This page was last modified on 30 June 2008, at 19:31. This page has been accessed 7,247 times.

3

Electrostatics - Biowerkzeug Wiki

http://wiki.biowerkzeug.org/index.php/Electrostatics

A non-exhaustive list of codes available to the academic community to perform calculations of electrostatic fields, typically solving the Poisson-Boltzmann equation. Or approximating it using the Generalized Born method. Free for academic users. Can also do Brownian Dynamics). PBEQ module, can also use APBS. Retrieved from " http:/ wiki.biowerkzeug.org/index.php/Electrostatics. This page was last modified on 30 June 2008, at 15:18. This page has been accessed 5,471 times.

4

Analysis software - Biowerkzeug Wiki

http://wiki.biowerkzeug.org/index.php/Analysis_software

Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. This list can act as a starting point. For most advanced uses, however, one will probably have to write analysis code in python. Or any other language that "gets the job done". General purpose mathematical packages. Many of the MD packages. Come with their own analysis tools or scripting language. Sometimes it is possible to convert data formats. From Alan Grossfield's lab p...

5

Membrane proteins - Biowerkzeug Wiki

http://wiki.biowerkzeug.org/index.php/Membrane_proteins

Setting up membrane protein simulations. Decide on the size of the protein/membrane system. Obtain parameters (for lipids see, for instance, Lipidbook. Choose a transmembrane protein insertion method. Retrieved from " http:/ wiki.biowerkzeug.org/index.php/Membrane proteins. This page was last modified on 22 May 2010, at 10:13. This page has been accessed 6,880 times.

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