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Molecular Dynamics Analysis Toolkit

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Molecular Dynamics Analysis Toolkit. Karl Debiec and Nick Rego Chong Group Department of Chemistry August 30 th 2013. Molecular Dynamics Simulation. Computer simulation of physical motions of atoms & molecules Applications in physics, chemistry, biology

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Molecular Dynamics Analysis Toolkit

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  1. Molecular Dynamics Analysis Toolkit Karl Debiec and Nick Rego Chong Group Department of Chemistry August 30th 2013

  2. Molecular Dynamics Simulation • Computer simulation of physical motions of atoms & molecules • Applications in physics, chemistry, biology • Several different programs developed by different groups • Output to diverse text and binary formats

  3. Cross-Platform Tools • Several tools exist for reading and analyzing different formats • Allows one analysis function to be written for multiple formats • These leave data storage and organization up to the user Loos

  4. Molecular Dynamics Analysis Toolkit • Streamlines analysis of MD simulations • Provide location of simulation and list of analyses • Figures out what needs to be done • Splits analyses across multiple cores • Stores results in HDF5 database • Wraps around existing tools, provides simple interface • Written in Python for Linux/OSX • Version controlled

  5. Goals for Capstone Project • Currently parses logs and analyzes external coordinate files

  6. Goals for Capstone Project • Currently parses logs and analyzes external coordinate files • Parse and store simulation configuration files (1-2 weeks)

  7. Goals for Capstone Project • Currently parses logs and analyzes external coordinate files • Parse and store simulation configuration files (1-2 weeks) • Copy atomic coordinates into database (1-2 weeks)

  8. Goals for Capstone Project • Currently parses logs and analyzes external coordinate files • Parse and store simulation configuration files (1-2 weeks) • Copy atomic coordinates into database (1-2 weeks) • Analyze either internal or external coordinates (6 weeks)

  9. Goals for Capstone Project • Currently parses logs and analyzes external coordinate files • Parse and store simulation configuration files (1-2 weeks) • Copy atomic coordinates into database (1-2 weeks) • Analyze either internal or external coordinates (6 weeks) • Copy binary restart file to allow simulation extension (2 weeks)

  10. Project Management • Work with myself, Nick Rego, and Professor Lillian Chong • Weekly meetings • Collaboration via BitBucket • If interested of have questions contact me at ktd3@pitt.edu • Check out code at https://bitbucket.org/karl_debiec/molecular-dynamics-analysis-toolkit

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