Desmond Tutorial

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Desmond Tutorial 4. Preparing a Desmond simulation with the System Builder . . . . . . . . . . . . . . . . 43 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Selecting Solutes and Solvents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 Defining the Simulation Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 System Builder Output File Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 Adding Ions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 Generating the Solvated System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 Setting Up Membrane Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 5. Finishing Preparations for Desmond Simulation . . . . . . . . . . . . . . . . . . . . . . . . 57 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Generating Force Field Parameters with Viparr . . . . . . . . . . . . . . . . . . . . . 57 Specifying Desmond Simulation Parameters. . . . . . . . . . . . . . . . . . . . . . . 60 Using the Run Desmond facility in Maestro . . . . . . . . . . . . . . . . . . 61 Editing the Desmond Conguration File Directly . . . . . . . . . . . . . . . . 63 6. Running Desmond Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 Running Simulations from the Desmond Window . . . . . . . . . . . . . . . . . . . 65 Running Simulations from the Command Line . . . . . . . . . . . . . . . . . . . . . 66 Running MultiSim jobs from the Command Line . . . . . . . . . . . . . . . . . . . . 67 7. Preparing Free Energy Perturbation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 Setting Up an FEP Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 Using Maestro To Generate A Desmond Configuration File . . . . . . . . . . . . . . 75 Running FEP Simulations from the Command Line . . . . . . . . . . . . . . . . . . 76 Adjusting the Conformation of the Mutant . . . . . . . . . . . . . . . . . . . . . . . 77 Creating a Custom Fragment Group . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 8. Visualization and Analysis using Maestro. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 Animating Desmond Trajectories with the Trajectory Player . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 Performing Simulation Quality Analysis . . . . . . . . . . . . . . . . . . . . . . . . . 83 9. Analyzing Trajectories Using VMD. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 The VMD Python Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 Loading and Viewing Trajectories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86 vi D. E. Shaw Research September 2008
Loading Files from the Command Line. . . . . . . . . . . . . . . . . . . . . 86 Loading Files from the GUI . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 Loading files from the scripting interface . . . . . . . . . . . . . . . . . . . 88 Getting information about snapshots. . . . . . . . . . . . . . . . . . . . . . . . . . . 89 Atom selections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 Snapshots. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 Writing structures and trajectories . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 Analyzing whole trajectories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93 Big trajectories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94 10. Documentation Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 September 2008 D. E. Shaw Research vii
Page 1 and 2: Desmond Tutorial Desmond Version 2.
Page 3 and 4: Preface Intended Audience This tuto
Page 5 and 6: from outermost to innermost, separa
Page 7: Contents Preface . . . . . . . . .
Page 11 and 12: List of Figures Figure 1.1: Simulat
Page 13 and 14: 1 Desmond Tutorial Introducing Desm
Page 15 and 16: Desmond Tutorial Tutorial Steps Fig
Page 17 and 18: Desmond Tutorial Tutorial Steps 3.
Page 27 and 28: Desmond Tutorial Tutorial Steps Sys
Page 31 and 32: 2 Learning the Maestro- Desmond Env
Page 33 and 34: Learning the Maestro-Desmond Enviro
Page 41 and 42: 3 Preparing Proteins with Missing R
Page 43 and 44: Preparing Proteins with Missing Res
Page 55 and 56: 4 Preparing a Desmond simulation wi
Page 57 and 58: Preparing a Desmond simulation with
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Preparing a Desmond simulation with
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5 Finishing Preparations for Desmon
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Finishing Preparations for Desmond
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6 Running Desmond Simulations Overv
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Running Desmond Simulations Running
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7 Preparing Free Energy Perturbatio
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Preparing Free Energy Perturbation
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8 Visualization and Analysis using
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Visualization and Analysis using Ma
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9 Analyzing Trajectories Using VMD
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Analyzing Trajectories Using VMD Lo
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Analyzing Trajectories Using VMD Ge
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Analyzing Trajectories Using VMD Ge
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Analyzing Trajectories Using VMD An
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Analyzing Trajectories Using VMD Bi
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10 Documentation Resources Detailed
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Desmond Tutorial

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