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Molecular Dynamics Analysis ToolkitKarl Debiec and Nick RegoChong GroupDepartment of ChemistryAugust 30th 2013

Computer simulation of physical motions of atoms & moleculesApplications in physics, chemistry, biologySeveral different programs developed by different groupsOutput to diverse text and binary formatsMolecular Dynamics Simulation

Loos

Several tools exist for reading and analyzing different formatsAllows one analysis function to be written for multiple formatsThese leave data storage and organization up to the userCross-Platform ToolsStreamlines analysis of MD simulationsProvide location of simulation and list of analysesFigures out what needs to be doneSplits analyses across multiple coresStores results in HDF5 database

Wraps around existing tools, provides simple interface

Written in Python for Linux/OSXVersion controlledMolecular Dynamics Analysis Toolkit

Goals for Capstone ProjectCurrently parses logs and analyzes external coordinate files

Goals for Capstone ProjectCurrently parses logs and analyzes external coordinate filesParse and store simulation configuration files (1-2 weeks)

Goals for Capstone ProjectCurrently parses logs and analyzes external coordinate filesParse and store simulation configuration files (1-2 weeks)Copy atomic coordinates into database (1-2 weeks)

Goals for Capstone ProjectCurrently parses logs and analyzes external coordinate filesParse and store simulation configuration files (1-2 weeks)Copy atomic coordinates into database (1-2 weeks)Analyze either internal or external coordinates (6 weeks)

Goals for Capstone ProjectCurrently parses logs and analyzes external coordinate filesParse 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)Work with myself, Nick Rego, and Professor Lillian ChongWeekly meetingsCollaboration 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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