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3. From the Calculations menu, point to MM2, and choose Minimize Energy. The Minimize Energy dialog box appears. 4. Set the convergence criteria using the following options:. Administrator Minimum RMS Gradient If you want to … Then … specify the convergence criteria for the gradient of the potential energy surface Enter a value for Minimum RMS Gradient. If the slope of the potential energy surface becomes too small, then the minimization has probably reached a local minimum on the potential energy surface, and the minimization terminates. The default value of 0.100 is a reasonable compromise between accuracy and speed. Reducing the value means that the calculation continues longer as it tries to get even closer to a minimum. Increasing the value shortens the calculation, but leaves you farther from a minimum. Increase the value if you want a better optimization of a conformation that you know is not a minimum, but you want to isolate for computing comparative data. 148•MM2 and MM3 Computations CambridgeSoft Minimize Energy
If you want to … Then … watch the minimization process “live” at each iteration in the calculation store each iteration as a frame in a movie for replay later Select Display Every Iteration. NOTE: Displaying or recording each iteration adds significantly to the time required to minimize the structure. Select Record Every Iteration. view the value of each measurement in the Output window Select Copy Measurements to Output. restrict movement of a selected part of a model during the minimization Select Move Only Selected Atoms. Constraint is not imposed on any term in the calculation and the values of any results are not affected. NOTE: If you are planning to make changes to any of the MM2 constants, such as cutoff values or other parameters used in the MM2 force field, please make a backup copy of the parameter tables before making any changes. This will assure that you can get back the values that are shipped with Chem3D, in case you need them NOTE: Chem3D guesses parameters if you try to minimize a structure containing atom types not supported by MM2. Examples include inorganic complexes where known parameters are limited. You can view all parameters used in the analysis using the Show Used Parameters command. See “Showing Used Parameters” on page 160. Running a Minimization To begin the minimization of a model: • Click Run. TIP: In all of the following minimization examples, you can use the MM2 icon on the Calculation toolbar instead of the Calculations menu. The Output window appears when the minimization begins, if it was not already opened. The data is updated for every iteration of the computation, showing the iteration number, the steric energy value at that iteration, and the RMS gradient. If you have not selected the Copy Measurements to Output option, only the last iteration is displayed. After the RMS gradient is reduced below the requested value, the minimization ends, and the final steric energy components and total appear in the Output window. ChemOffice 2005/Chem3D MM2 and MM3 Computations • 149 Minimize Energy
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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 Specifying Properties
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