Desmond Tutorial

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Desmond Tutorial Finishing Preparations for Desmond Simulation 64 D. E. Shaw Research September 2008
6 Running Desmond Simulations Overview NOTE You can run a Desmond simulation from the Desmond window or the command line. Before running a simulation you should check the Relax the model system before simulation option in the Desmond window. As discussed earlier, Desmond should perform structure relaxation to prepare a molecular system for production‐quality MD simulation. Maestroʹs built‐in relaxation protocol includes two stages of minimization (restrained and unrestrained) followed by four stages of MD runs with gradually diminishing restraints. The relaxation parameters may also require edits. The relaxation protocol is written to a .cmj command file (Chorus multi‐job file) which can be run from the command line (see “Running MultiSim jobs from the Command Line” on page 67). You can manually adjust the relaxation parameters by hand‐editing the .cmj file. If you decide to run the simulation from the Desmond window, you will be limited to use the built‐in OPLS‐AA force field for relaxation. Ideally, Desmond simulations should be run using the same force field for relaxation that is used for equilibration and simulation. Currently, if you run the simulation using Viparr you will need to run it from the command line. Running Simulations from the Desmond Window 1. Click the Start button at the bottom of the Desmond window to launch Desmond simulation jobs directly from the Maestro interface. The Desmond-Start window appears as shown in Figure 6.1. September 2008 D. E. Shaw Research 65
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Desmond Tutorial Desmond Version 2.
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Preface Intended Audience This tuto
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from outermost to innermost, separa
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Contents Preface . . . . . . . . .
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Loading Files from the Command Line
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List of Figures Figure 1.1: Simulat
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1 Desmond Tutorial Introducing Desm
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Desmond Tutorial Tutorial Steps Fig
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Desmond Tutorial Tutorial Steps 3.
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Desmond Tutorial Tutorial Steps 11.
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Page 25 and 26: Desmond Tutorial Tutorial Steps 18.
Page 27 and 28: Desmond Tutorial Tutorial Steps Sys
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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
Page 69 and 70: 5 Finishing Preparations for Desmon
Page 71 and 72: Finishing Preparations for Desmond
Page 73 and 74: Finishing Preparations for Desmond
Page 75: Finishing Preparations for Desmond
Page 79 and 80: Running Desmond Simulations Running
Page 81 and 82: 7 Preparing Free Energy Perturbatio
Page 83 and 84: Preparing Free Energy Perturbation
Page 93 and 94: 8 Visualization and Analysis using
Page 95 and 96: Visualization and Analysis using Ma
Page 97 and 98: 9 Analyzing Trajectories Using VMD
Page 99 and 100: Analyzing Trajectories Using VMD Lo
Page 101 and 102: Analyzing Trajectories Using VMD Ge
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Page 105 and 106: Analyzing Trajectories Using VMD An
Page 107 and 108: Analyzing Trajectories Using VMD Bi
Page 109 and 110: 10 Documentation Resources Detailed
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Desmond Tutorial

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