You will be performing calculations on a remote workstation. In many cases you can create the input file on the remote workstation using a molecular editor such as MOLDEN and a text editor such as nedit. In other times, you may need to transfer files back and forth between the workstation and the SGI machine you are sitting at. You can transfer files between computers using File Transfer Protocol, or FTP. You can access your files from the workstation by opening an ftp connection to the SGI file server (the address will be given in the class). After opening the FTP connection, navigate to your directory on the SGI file server by typing cd PERM where PERM is your perm number and hit enter. The commands get and put transfer files between computers. For example, if you have created an input file named butane.dat on the SGI machine, you can transfer this file to the workstation by typing get butane after opening the ftp connection from the workstation. Similarly, if the calculation has produced the output file butanbe.out, you can transfer it to the SGI machine using the FTP command put butane. You can exit the ftp program by typing bye.
You will be using a computational chemistry program Gaussian03 to perform the semiempirical calculations. Gaussian is one of the most commonly used computational chemistry programs and it is important that you learn well how to use it. One valuable resource is their on-line technical documentation.
Open the input file that contains the molecular geometry either in the XYZ format or in the Z-Matrix format in a text editor. For example, if the geometry specification for butabe is saved in the file butane.dat, type nedit butane.dat ) and insert the following block of lines just before the structure definition.
%Mem=16MW # PM3 Opt=CalcAll Butane in anti conformation, PM3 geometry optimization for learning semiempirical methods. 0 1
Inspect your file. A typical Gaussian input file will have a section that allocates computational resources (Link 0 commands that start with %) followed by the route section (lines that start with #), the title section (free format text), and molecule specification. There are three blank lines: one separating the route section from the title section, the other separating the title section from the molecule specifications, and the last one at the end of the molecule specification. The section that you added tells the Gaussian program to allocate 16 megawords (128 MB) of memory and perform optimization while evaluating the Hessian at each point. It also specifies the charge (0) and spin multiplicity (1) for the molecule. Both the charge and the spin multiplicity are integers. Charge is the total charge of the system (e.g. zero for a zwitterionic amino acid) and the multiplicity is 1 for closed-shell molecules in the ground electronic state. Multiplicity is 2 for single radicals and 3 for diradicals, such as molecular oxygen.
Excecute the calculation. You can either call the program directly as in g03 < input.dat > output.out & or submit your calculation to the queue using the subg03 command.