Desmond Tutorial

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Desmond Tutorial Analyzing Trajectories Using VMD 96 D. E. Shaw Research September 2008
10 Documentation Resources Detailed Desmond documentation can be found in the D. E. Shaw Research Desmond User Guide. Schrödingerʹs Desmond documentation includes the Quick Start Guide and the Desmond User Manual: $SCHRODINGER/docs/desmond/quick_start/des20_quick_start.pdf and $SCHRODINGER/docs/desmond/user_manual/des20_user_manual.pdf The documentation is also available by choosing Help > Manuals Index in Maestro. Maestro documentation can be found online at www.schrodinger.com and context specific online help can be brought up in any Maestro panel, which has a Help button. The complete Maestro documentation set includes: $SCHRODINGER/docs/maestro/overview/mae85_overview.pdf, $SCHRODINGER/docs/maestro/ref_manual/mae85_command_reference.pdf, $SCHRODINGER/docs/maestro/tutorial/mae85_tutorial.pdf, $SCHRODINGER/docs/maestro/user_manual/mae85_user_manual.pdf. The full ASL (atom specification language) documentation can be found in: $SCHRODINGER/docs/maestro/help/mae85_help/misc/asl.html The documentation of Prime can be found at $SCHRODINGER/docs/prime/quick_start/pri20_quick_start.pdf and $SCHRODINGER/docs/prime/user_manual/pri20_user_manual.pdf September 2008 D. E. Shaw Research 97
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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 Sys
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2 Learning the Maestro- Desmond Env
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Learning the Maestro-Desmond Enviro
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3 Preparing Proteins with Missing R
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Preparing Proteins with Missing Res
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4 Preparing a Desmond simulation wi
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Page 77 and 78: 6 Running Desmond Simulations Overv
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
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Page 97 and 98: 9 Analyzing Trajectories Using VMD
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