Geometry optimisation using Gaussian

This exercise follows the drylab Building Z matrices using Molden and uses the Z matrices for [PCl4]+, PCl5 and [PCl6]- saved in your unix filespace then as .com files.  You will now use the modelling program Gaussian, running in unix, to optimise the geometry of these species, starting from these Z matrices.  Besides writing a .log file of all the results it calculates, which can be read by human beings as well as by Molden, Gaussian also saves a checkpoint file .chk in machine-readable code, for its own future use.  This contains much more detail of molecular orbitals etc..  In the final drylab you may do the last exercise in this series, in which Gaussian will read the checkpoint files it saves now, and carry out vibrational analysis calculations to predict stretching frequencies.

Screen editors in unix

Making a command file for Gaussian, to optimise the geometry of PCl5

Running Gaussian

For running a modelling job of any size, Gaussian is normally used in a 'batch' environment, in which your job queues for the large resources required.  However, the current jobs are so small, because you are using a semi-empirical method on a small molecule, rather than doing ab initio calculations, that you can run Gaussian simply in the background from your present unix signon.  The essential is that you should remember to put the & to cause a background process, on the end of the command line, before you press Enter

Looking at the output from Gaussian

[PCl6]- and [PCl4]+