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sxguoch银虫 (小有名气)
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如何使用Oniom给计算制定分层
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我想请教Gaussian如何使用Oniom给计算制定分层，然后对每一层进行优化呢？ 谢谢赐教！ |
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要结合GassView使用，因GaussView里面带了这个功能 具体参见GaussView里面的例子 Assigning Atoms to ONIOM Layers in a Small Peptide Chain Note: This example is devised for its illustrative clarity rather than for scientific interest. 1. Create a peptide chain containing these amino acids: Phe-Ala-Gly. Choose the Amino-Terminal Phenylalanine, Central Fragment Alanine and Carboxyl-Terminal Glycine. 2. Assign all atoms to the Low Layer. Select Assign Layer from the Edit menu, and then click Select All. Verify that current layer is set to Low. The display will look similar to the following figure. Click Apply. 3. Assign the following atoms to the Medium layer: all atoms in Ala, carbons in Ring in Phe and atoms up to the double bond in Gly: Select the central carbon atom in Ala. Click in the right end of Expand Selection and add more atoms (two or more times). Adding too few atoms is usually easier than adding too many. Click Apply. Add additional atoms (select and then click Apply) as necessary until the selection is correct as in the following figure. Use the center mouse button to add atoms to the selection as needed, and then click Apply to confirm, repeating as needed. The atoms in the Medium layer are now displayed as tubes and the ones in the Low layer are in wireframe in the display: 4. Assign the following atoms to the High layer: all atoms in Ala, including heavy atoms bonded to them. Click the central carbon in Ala. Change Using field to Distance. Click twice at the right end of Expand selection. The display will be as in the following figure: Click Apply. The display is as in the following figure: Completed ONIOM-Assigned Molecule Remove the hydrogen atom that was just placed into the high layer by selecting it and then placing it in the Medium layer. Click Close. The atom layer assignment is now complete. 2.2.2.2 Setting Up an ONIOM Job This example uses the molecule that was built and the layers that were defined in the final example in the Building Tutorial, and it continues on from those steps. 1. Select Gaussian from the Calculate menu. 2. Click on Multilayer ONIOM Model. Three tabs appear (High, Medium, and Low) in the Method section, which you can use to select the methods for treating each layer of atoms. 3. Click on the High tab, then select an RHF/6-31G job. 4. Click on the Medium tab, then select a Restricted AM1 job. 5. Click on the Low tab and specify a molecular mechanics calculation using the Amber force field. 6. The following figure (Gaussian ONIOM Job Setup Example) shows these three tabs in the correct settings (superimposed below one another): These settings place the following line in the job's route section: # ONIOM=(RHF/6-31G:RAM1:Amber) You can now go on to fill out the rest of the dialog box, and the job will be ready to be saved and run. Assigning Atoms to ONIOM Layers in a Small Peptide Chain |
2楼2007-11-19 17:31:17
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3楼2007-11-21 22:52:46
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4楼2007-11-22 11:07:46
