GaussView 6 can perform a confrontational search for conformations using the GMMX add-on module. You can set up a search using one or both of the following available search methods:
- In a Cartesian search, each of the heavy atoms is moved by some random distance in each of the X, Y and Z dimensions. This is a good method for exploring the conformational space about a local minima.
- With the Bonds method, each of the selected bonds is rotated by some random amount. This normally provides large changes in the conformation of the molecule, and it is a good method for hopping between local minima.
- For ring systems, the Ringmaker strategy of Still is included in the Bonds method. This involves breaking one bond in a ring, rotating about the remaining bonds, and then trying to reclose the ring. If the bond length or the bond angles of the reclosed ring are not reasonable, the conformation is rejected, and a new attempt is made. This method works well with flexible rings of size 8 or larger. Rings of limited flexibility, such as fused rings or rings with double bonds, do not work well and should not be included in a ring search. These systems will work fine with just the Cartesian search method.
Once GMMX completes, all of the conformations found will be displayed in a list, and they can be opened as a single molecule group. You can also display an energy plot for the set of conformations.
