Chem3D 8.0 Manual - CambridgeSoft

inorganic complexes where known parameters arelimited. You can view all parameters used in theanalysis using the Show Used Parameterscommand. See “Showing Used Parameters” onpage 151.Running a MinimizationTo begin the minimization of a model:• Click Run.The Message Controller appears when theminimization begins. The is updated for everyiteration of the computation, showing theiteration number, the steric energy value at thatiteration, and the RMS gradient.After the RMS gradient is reduced below therequested value, the minimization ends, and thefinal steric energy components and total appearin the Messages table.Intermediate status messages may appear in theMessages window. A message appears if theminimization terminates abnormally, usuallydue to a poor starting conformation.To interrupt a minimization that is in progress:• Click Stop in the Movie Controller.The minimization and recording stops.Queuing MinimizationsYou can start to minimize several models withoutwaiting for each model to finish minimizing. If acomputation is in progress when you beginminimizing a second model, the minimization of thesecond model is delayed until the first minimizationstops.If you are using other applications, you can runminimization with Chem3D in the background. Youcan perform any action in Chem3D that does notchange the position of an atom or add or delete anypart of the model. For example, you can movewindows around during minimization, changesettings, or scale your model.Minimizing EthaneEthane is a particularly straightforward example ofminimization, because it has only oneminimum-energy (staggered) and onemaximum-energy (eclipsed) conformation.To minimize energy in ethane:1. From the File menu, choose New ModelAn empty model window appears.2. Click the Text Building tool.3. Click in the model window.A text box appears.4. Type CH3CH3 and press Enter.A model of Ethane appears.5. From the Object menu, point to Show SerialNumbers, and then choose Show.6. From the MM2 menu, choose Minimize Energyand click Run.The calculation is performed. Messages appearand the last one appears in the Messagecontroller.To view all the messages:• Click the expansion button in the Messagewindow.The values of the energy terms shown below areapproximate and can vary slightly based on thetype of processor used to calculate them.Chem3D 8 Chapter 10: MM2 Computations • 141Minimize Energy