the goodman group
university of cambridge  


   cerius2

The Silicon Graphics Teaching Laboratory
has been replaced by the
Chemi cal Information Laboratory
and this information is for historical interest only

Cerius2

Cerius2 is available. To use it, type cerius on any of the Silicon Graphics Teaching Laboratory Computers.

The license will only allow a very limited number of people to run Cerius2 concurrently, so it is possible that you will get a license error. If this occurs, try again later.

The research groups that contributed towards the cost of this license have priority. Do not be surprised if you are asked to stop a calculation to allow a higher priority calculation to begin.

Cerius2 is a product of Molecular Simulations Incorporated (MSI).

Diagram of Cerius2 Screen

The program has three main windows, the Main Screen where molecules are displayed, the Text Port where messages appear, and the Controls, which give you access to a wide range of menus and control panels. Here is an example of what you may see in the Controls window:

Controls window

The options along the top of the Controls window give you access to general commands, such as loading and saving molecules (models), and exiting from the program. The Help menu provides an introduction to the program.

The second row of commands control the appearance of the screen. The left hand button will allow you to change from a STICK representation (illustrated) to ball and stick, space filling, or various others. The second button from the right hand side of this row will hide all the control panels that may have appeared. This is very useful for tidying up the screen, and has no other effect on what you are doing.

The rest of the left hand side of the Controls window allows you to manipulate several molecules at the same time. In this example, only one molecule is present (Model1), but you may build up any number of these, and decide which should be visible, whether to quarter the screen, or have one big picture surrounded by several small ones, or to devote the screen to a single molecule.

The right hand side of the screen is a list of tools that are available in each module. In the illustration, BUILDERS 1 is the module selected, and this gives access to five tools (amorphous builder, polymer builder, interface builder, surface builder and crystal builder). Clicking on BUILDERS 1 gives a list of the other modules. We do not have licenses for all of the tools. Anything that is shown in light grey is not available.

Manipulating Molecules

     left mouse button     :   select atoms
     middle mouse button   :   translate molecule
     right mouse button    :   rotate molecules

Building Molecules

The easiest way to build molecules is to use the 3D sketcher in the Build menu. Selecting this option will give you a control panel to control atom types, bond orders, etc. Click on the ŒSketch with¹ icon (Three atoms forming a L) to draw a molecule in the Main Screen area. An option on this control panel is CLEAN. This will tidy up the molecule using a simple force field, so that the bond lengths and angles are approximately correct.

Energy Minimisation

Cerius2 has a variety of force fields available. Select the OFF SETUP module to investigate the different force field options. The default force field is UFF which stand for Universal Force Field. The OFF METHODS module will allow you to decide on minimisation options and to minimise a molecule. Cerius2 will plot a graph showing you how the energy is altering as the minimisation proceeds. This modules also allows you to do conformation searching and molecular dynamics.

Stopping Cerius2

Choose the Exit option of the File menu at the top left of the Controls window.



© Goodman Group, 2005-2017; privacy; last updated October 18, 2017

department of chemistry University of Cambridge