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Basic Exercises & Examples
Day 1 Workshop Exercises
Mar 11, 2012

  


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Energy Scan Exercise
An integrated exercise for some advanced OpenMM topics added by Lee-Ping (These are not the introductory Day 1 exercises; see Exercises & Examples.) In this exercise, we perform an energy scan to find the interaction energy between formaldehyde and water for two force fields - AMOEBA and OPLS-AA. High-accuracy ab initio benchmark data is included. Topics covered are: - Creating custom force fields - Manually specifying molecular topology - Saving and loading simulations using the Serializer - Extracting physical variables from a simulation state - Customizing simulations with elementary Python programming Package contains: EnergyScan.py = exercise script with prompts fml.xlsx = Excel spreadsheet with force field parameters Amoeba.xml = pre-built Amoeba system tip3p.xml = copy of TIP3P force field file input.pdb = input PDB file AnswerKey/Answer.py = the fully functioning script AnswerKey/fml.xml = the formaldehyde force field XML file PDBFiles/x[01-51].pdb = a series of MP2/aug-cc-pVTZ optimized geometries of a water/formaldehyde complex
Initial upload
Mar 12, 2012

Updates will be released if we find bugs / problems :)  


Free Energy Scripts
Scripts
Mar 14, 2012

  


Protein-Ligand Simulation
Sample scripts using AMBER tools
Mar 13, 2012

  


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Slides, Videos, and Handouts
OpenMM Videos
Jun 01, 2012

Videos of various presentations given at the OpenMM workshop held on March 12-13, 2012.  

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