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Gaussian 03 is the latest in the Gaussian series of electronic structure programs. Gaussian 03 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest. | Gaussian 03 is the latest in the Gaussian series of electronic structure programs. Gaussian 03 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest. | ||
Revision as of 13:04, 12 June 2009
go back to Main Page, Computational Resources, Chemistry & More, Computational Codes
Gaussian 03 is the latest in the Gaussian series of electronic structure programs. Gaussian 03 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.
Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures. This article introduces several of its new and enhanced features.
GAUSSIAN was first written by John Pople and released in 1970. According to the manual, it can deal with different computational approaches: molecular mechanics (AMBER, UFF, DREIDING), semi-empirical calculations (AM1,PM3,CNDO,INDO,MINDO/3,MNDO), SCF methods (Restricted, Unrestricted, and Restricted Open-shell Hartree-Fock), Møller-Plesset perturbation theory, DFT methods (Hybrid functionals, exchange functionals and correlation functionals), ONIOM (QM/MM method), Complete Active Space (CAS) and Multi-Configurational Self-Consistent Field calculations, Coupled Cluster calculations, QCI methods and Quantum chemistry composite methods.
Nearly everything you need to know can be found on the Gaussian's homepage, 1 and the on-line manual, [2]]
Installing Gaussian in your local computer
It is sometimes useful to be able to run short calculations on your local machine. Although this should not be done systematically to avoid burning out the machine.
One option is to compile the code (potentially painful).
Another option is to copy a pre-compiled version following the instructions below. It will not run optimally for your machine, but ...
Installing Gaussian on your local computer
Gaussian for beginners
If you are not familiar with Gaussian and Gaussview, it might be a good idea to run some "simple" calculations before starting your "own" project. Following the ling below you will find some exercices prepared for the Master on Computational Chemistry, which are a good starting point.
Graphical Interfaces
link to the GaussView help : [[1]] and Gauss View in the wiki Gauss View
Input Examples
In spite of the highly informative Gaussian homepage, it can sometimes be difficult for newcomers to get a quick overview of the program. In order to make the introduction to the program easier, input examples for several kinds of calculations will be presented in the following. In this way users new to the program can just copy, paste and modify the input examples and they will have a calculation ready to submit.
Optimisation from transition state geometries
Gaussian questions & answers
Links
http://www.gaussian.com/tech_top_level.htm
http://en.wikipedia.org/wiki/GAUSSIAN
Introduction and input/output explanation of PCM
http://www.cup.uni-muenchen.de/oc/zipse/compchem/solv/pcm.html
ABOUT SENDING CALCULATIONS :
- Checkpoints: They are big files which contain information such as the wave function or the geometry of finished calculations. They can not be edited with vi or nedit... (as they are written in binary) but the information they contain can be read by Gaussian. Although they might be very useful, to store them is not recommended if we are not sure about their utility.
In kimik, when the calculation finishes they are saved in the same directory as the output. For practical reasons while the calculation is running the checkpoint file should be saved in the Scrath. The submision script qs adds the lines
%chk=/scratch/filename.chk %nproc=XX (XX=nodes you asked for when using qs (qs 1 l g03 filename.in -> %nproc=1, whilst qs 1 q g03 filename.in -> %nproc=4)
automatically at the beginning of your input file creating a new input called filename.in.in. You should not include these lines in your input file when using qs, if not you will end up with two %chk= lines and two %nproc=.
ABOUT NBO: Natural Bond Orbital Analysis
It is recommended to use the keyword pop=nboread in the command line and at the end of the file $NBO 3CBONDS RESONANCE $END
http://www.chem.wisc.edu/~nbo5/ch3nh2.html
ABOUT PCM (CPCM, IPCM,..) :
- If you have one or more hydrogens "bonded" to two atoms (close to two atoms), the default parameters of PCM will not be able to compute the molecular cavity for them. There are two solutions for this problem:
-1- Use a different model to build up the cavity. Change the default UAO which does not explicitly consider hydrogens, by UHF, PAULING, BONDING.. which consider hydrogens explicitly.
-2- Use the keyword SPHEREONH = atom number of the hydrogen "bonded" to two atoms.
- An odd tip about PCM: If your PCM calculations work fine for most of your systems but they give problems to compute the cavity for few of them, with no apparent reason: try to modify slightly your coordinates.
A very small change of the coordinates may be enough to eliminate the problem. A good way to do that is to round the coordinates (i.e. from 2.347895 to 2.348) or re-optimize the molecule (the coordinates you will get will be slightly different). Even though that sounds quite stupid some times it is enough for the program to work.