Desmond Tutorial

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Desmond Tutorial Desmond Tutorial Table 1.1 Simulation files File desmond_job_multisim.log desmond_job-out.cms desmond_job_1-out.tgz desmond_job_2-out.tgz desmond_job_3-out.tgz desmond_job_4-out.tgz desmond_job_5-out.tgz desmond_job_6-out.tgz desmond_job.log desmond_job_mon.maegz desmond_job.ene desmond_job_trj desmond_job_trj.idx desmond_job_simbox.dat desmond_job.cpt Purpose The output file (the last frame of the trajectory). Compressed tar files containing all the information about the relaxation/equilibration stages. A general log of the simulation. A monitoring snapshot file (gzip compressed) that is used to periodically update the Workspace view in Maestro. The results of the production run are stored in the .ene file (energy terms). The .trj files store the trajectory snapshots in a _trj directory along with the simbox information. Simbox information. A checkpoint file that allows for the bitwise accurate restart of Desmond jobs that crashed for some reason. You can find the pertinent documentation in the Desmond User Guide and the Schrödinger Desmond User Manual listed in “Documentation Resources” on page 97. Trajectory analysis is covered in “Visualization and Analysis using Maestro” on page 81 and “Analyzing Trajectories Using VMD” on page 85. 18 D. E. Shaw Research September 2008
2 Learning the Maestro- Desmond Environment Overview The main Maestro window (shown in Figure 2.1) has a large workspace area, a main toolbar, called the main toolbar, along the left side of the window, a menu bar at the top of the window, and a command line at the bottom of the window. The workspace is where you build and manipulate molecular models. An information bar at the bottom of the window displays information about the molecular model currently in the workspace. The yellow cursor in the workspace is always labeled according to the current context. When a molecular structure is present in the workspace, all of the buttons in the main toolbar are active. If you move the cursor over any of the buttons, Maestro will display help text within a bubble. Most buttons have a small arrow in the lower right corner. Pressing and holding the left mouse button over this arrow displays more options. September 2008 D. E. Shaw Research 19
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 and 8: Contents Preface . . . . . . . . .
Page 9 and 10: Loading Files from the Command Line
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 29: Desmond Tutorial Tutorial Steps Fig
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 77 and 78: 6 Running Desmond Simulations Overv
Page 79 and 80: 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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