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Molecular Dynamics Analysis Toolkit

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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