GAUSSIAN: Difference between revisions
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Gaussian | Gaussian 09 is the latest in the Gaussian series of electronic structure programs. Gaussian 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. | 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. | ||
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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. | 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, [ | Nearly everything you need to know can be found on the Gaussian's homepage, [http://www.gaussian.com] and the on-line manual, [http://www.gaussian.com/g_tech/g_ur/g09help.htm] | ||
REMEMBER: '''You MUST use the "p" keyword''' for extra-print in '''all your calculations'''. | |||
==Versions == | |||
* [[G09]] | |||
[[ | * [[G03]] | ||
==Gaussian for beginners == | ==Gaussian for beginners == | ||
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[[ Optimisation from transition state geometries]] | [[ Optimisation from transition state geometries]] | ||
[[Solvent single point]] | |||
[[ | |||
== Gaussian related Tips:== | == Gaussian related Tips:== | ||
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* '''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. | * '''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 Scratch. The submision script qs adds the lines | In kimik/kimik2, 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 Scratch. The submision script qs adds the lines | ||
%chk=/scratch/filename.chk | %chk=/scratch/filename.chk | ||
% | %nprocs=XX (XX corresponds the ''type'' of node (4,8 or 12) you requested in qs | ||
The qs script does not add a line to specify memory usage, which must be done manually with the %Mem= command. | * '''Memory''': The qs script does not add a line to specify memory usage, which must be done manually with the "%Mem=" command. As a rule you should specify no more than 85% of a node's memory capacity to allow for normal OS operations, like disk writing and network access, otherwise you will start using swap space and slow down the calculation drastically (especially in frequency calculations) | ||
* '''--link1--'''; you can link calculations by writing the inputs one after the other and adding '''--link1--''' between them (one blank line before link1 and no blank line after). With this and the keywords geom=(checkpoint), guess=(read)... you could save time when doing solvent calculations or other. The outputs will be written in a single file. | |||
=== ABOUT NBO: Natural Bond Orbital Analysis === | === ABOUT NBO: Natural Bond Orbital Analysis === | ||
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http://www.chem.wisc.edu/~nbo5/ch3nh2.html | http://www.chem.wisc.edu/~nbo5/ch3nh2.html | ||
=== | === NMR parameters, the chemical shift === | ||
The '''NMR''' keyword can be added at the command line. It predicts NMR shielding tensors and magnetic susceptibilities (HF, DFT & MP2 methods). | |||
The '''GIAO''' method is used by default, and it is one of the recommended methods. Usually these calculations are performed with IGLO-II basis sets, altough other basis sets can also been used. | |||
- | To obtain the chemical shifts, the Isotropic Magnetic shielding (ppm) obtained from the Gaussian output, should be '''referenced to that of TMS''' (tetra-methylsilane) at the same level. i.e. at b3lyp/6-31g* basis set it is 31.92 ppm. | ||
δ(X) (ppm) = isotropic(TMS) – isotropic(X) | |||
=== Bader's analysis === | |||
If you would like to analyse your systems by using parameters of Bader's analysis (AIM Atoms in Molecules). You could use gaussian to get a .wfn file. To get it it is necessary to write output=wfn at the command line and the name of the wfn file at the end (after general basis sets).[[example_bader]] | |||
Afterwards you could use Xaim to locate critical points, or to plot the maps of density, laplacian, ... Prof. Carles Bo is one of the fathers of Xaim. Xaim is available on kimik and it can be download for free at | |||
http://www.quimica.urv.es/XAIM/ | |||
== Scripts == | |||
* [[energies]] | |||
* [[Macromodel_to_gaussian]] | |||
Latest revision as of 14:55, 30 October 2012
go back to Main Page, Computational Resources, Chemistry & More, Computational Codes
Gaussian 09 is the latest in the Gaussian series of electronic structure programs. Gaussian 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]
REMEMBER: You MUST use the "p" keyword for extra-print in all your calculations.
Versions[edit]
Gaussian for beginners[edit]
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[edit]
link to the GaussView help : [[3]] and Gauss View in the wiki Gauss View
Input Examples[edit]
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
[edit]
ABOUT SENDING CALCULATIONS :[edit]
- 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/kimik2, 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 Scratch. The submision script qs adds the lines
%chk=/scratch/filename.chk %nprocs=XX (XX corresponds the type of node (4,8 or 12) you requested in qs
- Memory: The qs script does not add a line to specify memory usage, which must be done manually with the "%Mem=" command. As a rule you should specify no more than 85% of a node's memory capacity to allow for normal OS operations, like disk writing and network access, otherwise you will start using swap space and slow down the calculation drastically (especially in frequency calculations)
- --link1--; you can link calculations by writing the inputs one after the other and adding --link1-- between them (one blank line before link1 and no blank line after). With this and the keywords geom=(checkpoint), guess=(read)... you could save time when doing solvent calculations or other. The outputs will be written in a single file.
ABOUT NBO: Natural Bond Orbital Analysis[edit]
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
NMR parameters, the chemical shift[edit]
The NMR keyword can be added at the command line. It predicts NMR shielding tensors and magnetic susceptibilities (HF, DFT & MP2 methods).
The GIAO method is used by default, and it is one of the recommended methods. Usually these calculations are performed with IGLO-II basis sets, altough other basis sets can also been used.
To obtain the chemical shifts, the Isotropic Magnetic shielding (ppm) obtained from the Gaussian output, should be referenced to that of TMS (tetra-methylsilane) at the same level. i.e. at b3lyp/6-31g* basis set it is 31.92 ppm.
δ(X) (ppm) = isotropic(TMS) – isotropic(X)
Bader's analysis[edit]
If you would like to analyse your systems by using parameters of Bader's analysis (AIM Atoms in Molecules). You could use gaussian to get a .wfn file. To get it it is necessary to write output=wfn at the command line and the name of the wfn file at the end (after general basis sets).example_bader
Afterwards you could use Xaim to locate critical points, or to plot the maps of density, laplacian, ... Prof. Carles Bo is one of the fathers of Xaim. Xaim is available on kimik and it can be download for free at
http://www.quimica.urv.es/XAIM/