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For brief introductions to using some of our software packages and examples on how to set up input files, please click on the following links.
Note: These software introductions only provide a guide to using the programs. Users are advised to refer to the corresponding user manual for full details. These pages will open in a new web browser window.
| ACES | ADF | Dalton | GAMESS-UK |
| GAMESS-US | Gaussian | GULP | |
| MOLCAS | MOLPRO | TURBOMOLE |
More software introductions will be added when they are available.
All of the example input and output files given are available for download in gzipped format. Gzip executables can be downloaded from here.
The following software packages have their own comprehensive tutorials. Please click on the following links to visit their official web sites.
| ABINIT | AMBER | AutoDock | CASTEP |
| CRYSTAL | DL_POLY | GROMACS | NAMD |
| NWChem | Quantum-ESPRESSO | SIESTA |
Below are some useful information on setting up a z-matrix, converting geometry file formats and basis sets.
How to set up a z-matrix?Most programs require the setting up of molecular system using z-matrix. The details on how to set one up are usually available from the individual program's user manual. However, it can be quite cumbersome when you are setting up for a large system.
The z-matrix Editor from MOLDEN will be very helpful to aid the set up of the z-matrix. MOLDEN is a pre- and post- processing program of molecular and electronic structure, and can be downloaded for free. The z-matrix Editor in MOLDEN lets the user create and/or manipulate structures on screen. The final structure can be saved as a z-matrix file or as a variety of Cartesian formats. The z-matrix Editor can also convert a xyz Cartesian coordinates file into z-matrix. For formats other than xyz Cartesian coordinates, OpenBabel can be used for converting the corresponding format into xyz Cartesian.
How to convert geometry file formats?In molecular modelling, sometimes we will encounter the needs to convert the molecular structure from one format to another, for example from pdb (Protein Data Bank) format to xyz Cartesian coordinates. One of the easiest way is to use a molecular visualisation manipulator to convert it, however, these are very expensive to purchase. One program that is freely available for this task is Open Babel. Open Babel is a molecular structure chemical toolbox. It is a program designed to interconvert a number of file formats currently used in molecular modelling. Open Babel is also capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file. Open Babel can be downloaded for free from this website: http://openbabel.sourceforge.net/. Open Babel is available on Magellan and can be accessed interactively via the runscript $CHEM/runopenbabel. More information on the Magellan implementation can be found in the man page, accessible by typing man runopenbabel.
Where to download basis sets?Nearly all programs require a different way for their basis sets specifications. It is possible to order basis set from the EMSL Basis Set Exchange (BSE). The BSE contains nearly all the currently available basis sets along with detailed references, so users can order basis sets from there as well as being able to trace the original publications. Basis sets that can be ordered from the BSE for the software available from the Service are GAMESS-US, GAMESS-UK, Gaussian, MOLPRO, MOLCAS, NWChem, ACES, Dalton and TURBOMOLE.