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If you want to … Then Click … Administrator Select the appropriate options: If you want to … Then Click … record each iteration as a frame in a movie for later replay track a particular measurement restrict movement of a selected part of a model during the minimization Record Every Iteration. Copy Measurements to Output. Move Only Selected Atoms. Constraint is not imposed on any term in the calculation and the values of any results are not affected. save a file containing the Time (in picoseconds), Total Energy, Potential Energy, and Temperature data for each step. To begin the computation: Click Save Step Data In and browse to choose a location for storing this file. The word “heating” or “cooling” appears for each step in which heating or cooling was performed. A summary of this data appears in the Message window each time a new frame is created. • Click Run. The computation begins. Messages for each iteration and any measurements you are tracking appear in the Output window. If you have chosen to Record each iteration, the Movie menu commands (and Movie toolbar icons) will be active at the end of the computation. The simulation ends when the number of steps specified is taken. To stop the computation prematurely: • Click Stop in the Computation dialog box. Computing the Molecular Dynamics Trajectory for a Short Segment of Polytetrafluoroethylene (PTFE) To build the model: 1. From the File menu, choose New. 2. Select the Text Building tool. 3. Click in the model window. 156•MM2 and MM3 Computations CambridgeSoft Molecular Dynamics
A text box appears. 4. Type F(C2F4)6F and press the Enter key. A polymer segment consisting of six repeat units of tetrafluoroethylene appears in the model window. To perform the computation: To review the results: 1. View the Output window to examine the measurement data included in the molecular dynamics step data. 2. Drag the Movie slider knob to the left until the first step appears. 1. Select C(2), the leftmost terminal carbon, then Shift+click C(33), the rightmost terminal carbon. 2. Choose Set Distance from the Measurement submenu of the Structure menu. A measurement for the overall length of the molecule appears in the Measurements table. 3. Choose Molecular Dynamics from the MM2 submenu of the Calculations menu. 4. Click the Job Type tab and click the checkbox for Copy Measurements to Output. If you want to save the calculation as a movie, select Record Every Iteration checkbox. 5. Click Run. When the calculation begins, the Output Window appears. To replay the movie: • Click Start on the Movie menu. The frames computed during the molecular dynamics calculation are played as a movie. Selected The C(2)-C(33) distance for the molecule before the molecular dynamics calculation began is approximately 9.4Å. 3. Scroll down to the bottom of the Output window and examine the C(2)-C(33) distance for the molecule at 0.190 picoseconds (which corresponds to frame 20 in the Movie slider of the model window). The C(2)-C(33) distance is approximately 13.7Å, 42% greater than the initial C(2)-C(33) distance. ChemOffice 2005/Chem3D MM2 and MM3 Computations • 157 Molecular Dynamics
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ChemOffice.Com ® ChemOffice ® Che
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Chapter 31: Changes and Audit Trail
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Administrator Tutorial 7: Docking M
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Administrator Connection Table . .
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Administrator Specifying Properties
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CS Software Problem Report For fast
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