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

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Mar 11, 2012
78 KB
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Source code
Hands-on exercises used during the workshop


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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 :)

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Mar 12, 2012
18 KB
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Application/binary


Free Energy Scripts
Scripts
Mar 14, 2012

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Apr 22, 2013
8 KB
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Source code
John Chodera's scripts for computing alchemical free energy in OpenMM

Apr 22, 2013
21 KB
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Source code
John Chodera's scripts for doing replica exchange in OpenMM


mdseriesmar2012
Protein-Ligand Simulation
Sample scripts using AMBER tools
Mar 13, 2012

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Mar 13, 2012
4 MB
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Other
Gert Kiss' sample scripts for parameterizing a protein-ligand system to be simulated in OpenMM


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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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Aug 02, 2012
127 MB
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Data/images/video
Vijay Pande's introduction and roadmap to OpenMM.

Jun 01, 2012
191 MB
Any
Data/images/video
Peter Eastman's presentation "Running Simulations with OpenMM".

Aug 02, 2012
149 MB
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Data/images/video
Diwakar Shukla leads the group through three simulation exercises.

Jun 01, 2012
266 MB
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Data/images/video
Peter Eastman's presentation "The OpenMM API".

Jun 02, 2012
132 MB
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Data/images/video
Peter Eastman's presentation "Custom Forces in OpenMM".

Jun 02, 2012
139 MB
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Data/images/video
Lee-Ping Wang's presentation "The AMOEBA Polarizable Force Field in OpenMM".

Jun 01, 2012
69 MB
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Data/images/video
Peter Eastman's presentation "Validating OpenMM".

Jun 01, 2012
277 MB
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Data/images/video
John Chodera's presentation "Alchemical free energy calculations and replica-exchange with OpenMM".

Previous Releases


Workshop Materials

Mar 13, 2012

Documentation Links

Mar 26, 2012
Vijay Pande's introduction to the OpenMM project and the project roadmap

Mar 13, 2012
Peter Eastman's presentation providing basics of running a simulation using the OpenMM application layer

Mar 13, 2012
Diwakar Shukla's introductory slides for running OpenMM simulation (basic) exercises

Mar 13, 2012
Peter Eastman's introduction to the OpenMM API, including a discussion of the Units Python module

Mar 13, 2012
Peter Eastman's presentation on creating custom forces in OpenMM

Mar 13, 2012
Lee-Ping Wang's introduction to the AMOEBA Polarizable Force Field as implemented in OpenMM

Mar 13, 2012
Peter Eastman's presentation explaining how OpenMM is validated

Mar 13, 2012
John Chodera's presentation on alchemical free energy and replica exchange with OpenMM


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