Chem3D Users Manual - CambridgeSoft

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. Administrator 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. The Molecular Dynamics dialog box appears with the default values. 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. 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. 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. 158•MM2 and MM3 Computations <strong>CambridgeSoft</strong> Molecular Dynamics
• 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. 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. ChemOffice 2005/<strong>Chem3D</strong> MM2 and MM3 Computations • 159 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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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Administrator • CambridgeSoft
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Administrator The Calculation Toolb
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Administrator 1. Right-click in the
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Administrator 30 •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 Determine the raw spi
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Administrator The following table d
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Administrator When Correct Atom Typ
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Administrator To use the same text
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Administrator Example 2. Building a
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Administrator copied into blank tab
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Administrator 3. Type the atom type
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Setting Serial Numbers this step, y
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Administrator New in Chem3D version
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Administrator Dragging moves atoms
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Administrator 3. Hold down the Shif
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To position a plane in your model p
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Administrator • Second Positioned
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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SOLUTIONS •Adds chemical data typ
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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MANAGEMENT • E-Notebook Enterpris
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DISCOVERY • Accessed through your
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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