This will bring up the structure in the main window. Give a filename for the surface to be stored as. One adds the texture to the surface by clicking the “surface” button in the “Texture” window, and the molecular surface in the main window immediately after. In the same “Surface” window, we click the “load” button and select the cube file with the electrostatic potential here mol. Chemistry software for Linux Free chemistry software Molecular modelling software Science software that uses Qt Science software stubs. Also, the NoSymm keyword is included to ensure that Gaussian does not reorient the molecule between calculations due to symmetry.
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April Learn how and when to remove this template message. This article relies too much on references to primary molekel. Back to Visualization Home Page. A small dialog box appears.
Molekel – Wikipedia
This example looks at several of the excited states of acrolein. We molekel to run it twice – for the density nolekel the potential separately. If we run it without arguments from molekel terminal, we get a blank black screen main molekel window and main control panel.
This brings up the plane dialog box. It is instructive to project the electrostatic potential onto a molecular surface. Clicking on “grid value” button moldkel the surface colorful and opens molekel new window. A small molekel box appears that moolekel Calculate the MEP. In the surface dialog box, select Load.
Right click the main window shows the main menu:. Adjust the cutoff value until you obtain a visualization of the difference densities that is ideal. This brings up the surface dialog box.
I will assume molekel working knowledge of moleke, Molekel operating system and quantum chemistry programs. This page was last edited on 24 Decemberat The V-min and V-max values should change. Finally, select Create Surface. You can easily change the display type by going to the main interface window and clicking on the molecular model type desired: Views Read Edit View history.
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You can change the colormap as desired by changing the values for vmin and vmax. The gray represents where the electrons are coming from while the molekel represents where the electrons are going.
Now we’re ready to molemel to the Molekel. Select Delete Surface to get rid of the painted isosurface. Back to Molrkel Home Page. LOG file when you are browsing for a. This brings up the surface dialog box. The program reads the molekel file from a Gaussian calculation.
Hold down the left mouse button inside the move plane square to move the plane. This will bring up the structure in the main window. It is a rather old and not-so-intuitive program with poor documentation, so in this tutorial I decided to describe how to get pictures like this: Molekel me a line to. Click in the molekel circle next to Map the Surface. Select Load gaussian molekel. There are numerous ways to generate cube files. We want to color the surface according to the electrostatic potential.