Molecular Dynamics Workshop Series, June 24-26, 2009
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Day 1 -- OpenMM
Geared towards developers who are interested in using the OpenMM library to enable their MD code to run on high performance computer architectures, such as GPUs. The current version of the freely downloadable OpenMM enables MD codes to run on NVIDIA and ATI GPUs, and has demonstrated speed ups of over 100X for implicit solvent simulations.[1]
Meeting Materials
Jun 24, 2009

  

Download Package

Documentation Links

Slides

OpenMMAPI.pdf
Jul 07, 2009
by Peter Eastman / Introduction to the OpenMM API

ExplicitSolvent.pdf
Jul 08, 2009
by Peter Eastman / Implementing explicit solvent simulations for the GPU

IntegratingOpenMM.pdf
Jul 08, 2009
by Michael Sherman / Example of integrating OpenMM into a simple MD code ("HelloNaCl" program)

WritingYourFirstProgram.pdf
Jul 07, 2009
by Michael Sherman / Explanation of the provided "HelloArgon" program

Videos

PandeIntroOpenMMRoadmap.mov
Aug 04, 2009
by Vijay Pande -- Introduction of OpenMM & Roadmap

KohlhoffProgrammingGPUs.mov
Aug 04, 2009
by Kai Kohlhoff -- Programming on GPUs

EastmanOpenMMAPI.mov
Aug 04, 2009
by Peter Eastman -- OpenMM API

ShermanPart1.mov
Aug 04, 2009
by Michael Sherman -- Writing your first program that uses the OpenMM API

ShermanPart2.mov
Aug 04, 2009
by Michael Sherman -- Integrating OpenMM into a simple MD code

EastmanCaseStudy.mov
Aug 04, 2009
by Peter Eastman -- OpenMM integration into GROMACS

EastmanIplExplSolv.mov
Aug 04, 2009
by Peter Eastman -- Explicit Solvent Simulations for the GPU

Other Materials

EnergyFunctions.pdf
Jul 08, 2009
List of the energy functions, as implemented within OpenMM

MeetingAgenda.pdf
Jul 08, 2009

PLEASE CITE THESE PAPERS

[1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872. (2009)


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Day 2 -- MSMBuilder
For researchers who want to analyze MD simulations, mapping out the metastable states of a molecule and the transition rates between them. You will learn about Markov State Models and why they are suitable for this, and use the MSMBuilder software[2] to automatically construct such models, as well as analyze and visualize them.
Workshop Materials
Jun 25, 2009

  

Download Package

Documentation Links

Slides

MSMBuilderIntroduction.pdf
Jul 09, 2009
by Greg Bowman / Introduction to MSM Builder + example with analytical 2D potential

AlanineDipeptideExample.pdf
Jul 09, 2009
by Xuhui Huang / Use MSM Builder to construct MSM for trajectory data + other functions within MSM Builder

Videos

PandeIntroToMSM.mov
Aug 06, 2009
by Vijay Pande -- Introduction to Markov State Models

BowmanMSMBuilderHandsOn.mov
Aug 06, 2009
by Greg Bowman -- Introduction to MSMBuilder (hands-on)

HuangMSMBuilderwithAlanine.mov
Aug 06, 2009
by Xuhui Huang -- Using MSMBuilder with Alanine Dipeptide (hands-on)

Other Materials

MSMBuilderTutorial.pdf
Jul 09, 2009
Tutorial with 2 examples: analytical 2D potential and trajectory data for alanine dipeptide

MSMBuilderWorkshopAgenda.pdf
Jul 08, 2009

PLEASE CITE THESE PAPERS

[2] GR Bowman, X Huang, and VS Pande, "Using generalized ensemble simulations and Markov state models to identify conformational states," Methods (accepted). (2009)


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Day 3 -- MD & Zephyr
For researchers interested in using MD in their research, including novices to MD. You will learn the theory behind MD and use the OpenMM Zephyr application, which makes it easy to run and visualize MD simulations. OpenMM Zephyr incorporates the OpenMM library, enabling acceleration of the simulations on GPUs.
Workshop Materials
Jun 26, 2009

  

Download Package

Documentation Links

Slides

OpenMMZephyrIntroduction.pdf
Jul 08, 2009
by Joy Ku / Run your first MD simulation using OpenMM Zephyr

ExploringOpenMMZephyr.pdf
Jul 09, 2009
by Joy Ku / Learn how to run MD simulations on GPUs and gain insight into setting up your own simulation

mdrun.pdf
Jul 09, 2009
by Mark Friedrichs / Use mdrun to to run simulations with additional parameter settings

Videos

PandeIntroToMD.mov
Aug 06, 2009
by Vijay Pande -- Introduction to molecular dynamics

KuIntroToOpenMMZephyr.mov
Aug 06, 2009
by Joy Ku -- Introduction to OpenMM Zephyr

KuExploringMoreZephyr.mov
Aug 06, 2009
by Joy Ku -- Exploring more OpenMM Zephyr features

PandeAdvanceTopics.mov
Aug 06, 2009
by Vijay Pande -- Introduction to advanced topics in molecular dynamics

FriedrichsUsingOpenMM.mov
Aug 06, 2009
by Mark Friedrichs -- Exercise: Using OpemMM/mdrun to run simulations with additional parameter settings

Other Materials

ZephyrUserManual.pdf
Jul 09, 2009
User guide for Zephyr + step-by-step instructions for using mdrun

ZephyrWorkshopAgenda.pdf
Jul 09, 2009


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Other Workshop Information
Links
Jul 09, 2009

  

Documentation Links

Link to workshop photos (URL)
Jul 09, 2009


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