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Administrator During dragging, the bond lengths and angles were deformed. To return them to the optimal values before minimizing: 1. Select all (Ctrl+A) and run Clean Up. Now run the minimization: 2. From the MM2 submenu of the Calculations menu, choose Minimize Energy and click Run. 3. When the minimization is complete, reorient the model using the Rotation bars to see the final chair conformation. NOTE: The values of the energy terms shown here are approximate and can vary slightly based on the type of processor used to calculate them. Molecular Dynamics Molecular Dynamics uses Newtonian mechanics to simulate motion of atoms, adding or subtracting kinetic energy as the model’s temperature increases or decreases. Molecular Dynamics allows you to access the conformational space available to a model by storing iterations of the molecular dynamics run and later examining each frame. Performing a Molecular Dynamics Computation To perform a molecular dynamics simulation: 1. Build the model (or fragments) that you want to include in the computation. This conformation is about 5.5 kcal/mole more stable than the twisted-boat conformation. For molecules more complicated than cyclohexane, where you don’t already know what the global minimum is, some other method is necessary for locating likely starting geometries for minimization. One way of accessing this conformational space of a molecule with large energy barriers is to perform molecular dynamics simulations. This, in effect, heats the molecule, thereby increasing the kinetic energy enough to surmount the energetically disfavored transition states. NOTE: The model display type you use affects the speed of the molecular dynamics computation. Model display will decrease the speed in the following order: Wire Frame< Sticks < Ball and Sticks< Cylindrical Bonds < Ribbons< Space Fill and VDW dot surfaces < Molecular Surfaces. 2. Minimize the energy of the model (or fragments), using MM2 or MOPAC. 3. To track a particular measurement during the simulation, choose one of the following: • Select the appropriate atoms, and choose Set Bond Angle or Set Bond Length on the Measurement submenu of the Structure menu. 4. Choose Molecular Dynamics on the MM2 submenu of the Calculations menu of the Calculations menu. 154•MM2 and MM3 Computations CambridgeSoft Molecular Dynamics
. The Molecular Dynamics dialog box appears with the default values. 5. Enter the appropriate values. 6. Click Run. Dynamics Settings Use the Dynamics tab to enter parameter values for the parameters that define the molecular dynamics calculations: • Step Interval—determines the time between molecular dynamics steps. The step interval must be less than ~5% of the vibration period for the highest frequency normal mode, (10 fs for a 3336 cm– 1 H–X stretching vibration). Normally a step interval of 1 or 2 fs yields reasonable results. Larger step intervals may cause the integration method to break down, because higher order moments of the position are neglected in the Beeman algorithm. • Frame Interval—determines the interval at which frames and statistics are collected. A frame interval of 10 or 20 fs gives a fairly smooth sequence of frames, and a frame interval of 100 fs or more can be used to obtain samples of conformational space over a longer computation. • Terminate After—causes the molecular dynamics run to stop after the specified number of steps. The total time of the run is the Step Interval times the number of steps. • Heating/Cooling Rate—dictates whether temperature adjustments are made. If the Heating/Cooling Rate check box is checked, the Heating/Cooling Rate slider determines the rate at which energy is added to or removed from the model when it is far from the target temperature. A heating/cooling rate of approximately 1.0 kcal/atom/picosecond results in small corrections which minimally disturb the trajectory. A much higher rate quickly heats up the model, but an equilibration or stabilization period is required to yield statistically meaningful results. To compute an isoenthalpic trajectory (constant total energy), deselect Heating/Cooling Rate. • Target Temperature—the final temperature to which the calculation will run. Energy is added to or removed from the model when the computed temperature varies more than 3% from the target temperature. The computed temperature used for this purpose is an exponentially weighted average temperature with a memory half-life of about 20 steps. Job Type Settings Use the Job Type tab to set options for the computation. ChemOffice 2005/Chem3D MM2 and MM3 Computations • 155 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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Administrator Undoing Changes . . .
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Administrator Chapter 28: Introduci
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Administrator Atom Properties . . .
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Administrator Deleting a Field Type
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Administrator Reaction Center . . .
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Administrator The following table d
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Administrator • Bond Angles—Dis
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Administrator The Building Toolbar
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Administrator The Calculation Toolb
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Administrator 1. Right-click in the
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Administrator 26 •Chem3D Basics C
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Administrator In the Measurements t
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Administrator Tutorial 7: Docking M
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Administrator To save the iteration
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Administrator Clean Up Structure or
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Administrator Refining a Model Afte
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Administrator New in Chem3D version
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Administrator 3. Hold down the Shif
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CONSULTING & Consulting & Services
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CS Software Problem Report For fast
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