Desmond Tutorial

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Desmond Tutorial Finishing Preparations for Desmond Simulation Figure 5.2 Advanced Options for simulation jobs Parameters for nonbonded interactions. Thermostat and barostat parameters. Controls output files for simulations. Parameters for setting harmonic restraints. Other parameters such as those defining atom groups. Multiple time step parameters and constraints. The Advanced Options window has several tabs: • Ensemble—Contains thermostat and barostat parameters. • Interaction—Contains parameters for computing non‐bonded interactions. • Restraint—Provides a table in which multiple sets of atoms can be subjected to harmonic restraint with a user‐defined force constant. Atom selection can be directly input as an ASL expression or you can click the Select button to bring up the Atom Selection dialog box. • Output—Includes the names of various Desmond output files, and allows you to specify how often these files are updated during the simulation. For example, different energy terms are recorded in the energy sequence file in user‐defined intervals. Snapshots of the simulation are periodically saved in the trajectory file and the entire simulation state is also saved at user‐defined intervals in a checkpoint file. Desmond simulations can be restarted from checkpoint files with bitwise accuracy. • Misc—Provides control over miscellaneous parameters, including the definition of atom groups. Currently, two different atom groups are recognized by Desmond. A `frozenʹ atom group means a set of atoms that move during the entire MD simulation as a rigid body. (NOTE: in Desmond, unfrozen atoms cannot be connected to frozen atoms). For example, an entire protein molecule can be frozen (during equilibration), but one cannot freeze only the heavy atoms, or just certain residues. In that case, restraints should be used. Also note that frozen atoms cannot be used with NPT simulations, because the Virial will be incorrect. The other atom group termed cm_moi is used to define parts of the system whose center of mass motion is set to zero. In most protein simulations the protein center of mass motion is set to zero to prevent the protein from translating and rotating in the simulation box. Atom 62 D. E. Shaw Research September 2008
Finishing Preparations for Desmond Simulation Specifying Desmond Simulation Parameters groups can be selected the same way as restraint groups, using ASL syntax or the Atom Selection dialog box. The Desmond window is filled in automatically with default parameter values. To configure your own default values so they are automatically presented in the Desmond window, set the desired values in the Desmond window and save it by clicking the Write button. Then, copy the resulting .cfg file to ~/.schrodinger/desmond10/desmond_default.cfg. The new default values take effect the next time you open the Desmond window. Detailed documentation of the Run Desmond facility can be found in the Schrödinger Desmond User Manual listed in “Documentation Resources” on page 97. Once you have set values for relevant parameters, you are ready to execute a simulation. Editing the Desmond Conguration File Directly The Desmond conguration file syntax is described in detail in the Desmond User Guide (see “Documentation Resources” on page 97). You can edit the Desmond conguration file directly. It can be useful to edit existing configuration files that were used in other projects. September 2008 D. E. Shaw Research 63
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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 Fig
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Page 31 and 32: 2 Learning the Maestro- Desmond Env
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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
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Page 69 and 70: 5 Finishing Preparations for Desmon
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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
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
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Page 109 and 110: 10 Documentation Resources Detailed
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Desmond Tutorial

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