GAUSSIAN 98
Gaussian 98 (G98) is a package of programs marketed by Gaussian, Inc. to be used for performing a variety of semi-empirical and ab initio molecular orbital (MO) calculations.
Citation
We currently have Gaussian 98, Revision A.9 running on the Research and Graphics clusters. If you have run G98 jobs on any of these clusters, you should cite Gaussian 98 using the information below:
Software
General information for all versions of Gaussian 98 is available herein. You must replace "Revision A.x" with the correct version designation for the G98 program that you use. (The Revision information can be found in the beginning of the output files.)
If you have run G98 jobs on the Research or Graphics Clusters, you should cite the following:
- Gaussian 98, Revision A.9,
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 1998. - NSF Grant CHE0091916 and gifts from the Intel Corporation
For Gaussian 98 Revisions Prior to A.10
Gaussian 98 (Revision A.x), M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P. M. W. Gill, B. G. Johnson, W. Chen, M. W. Wong, J. L. Andres, M. Head-Gordon, E. S. Replogle and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 1998.
For Gaussian 98 Revision A.10 and Later
Gaussian 98 (Revision A.1x),M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, P. Salvador, J. J. Dannenberg, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 2001.
Hardware
- Bohr and Graphics GFX clusters
NSF Grant CHE0091916 and gifts from the Intel Corporation - Moore cluster: TBA
- Computer teaching classroom: TBA
Access
Availability
Gaussian 98 is available on the following systems:
- Bohr cluster
- GFX cluster
- Moore cluster
- Computer Classroom - Room 1381
Instructions on how to access and use Gaussian 98 at the Chemistry Department are shown below:
Manual
G98 manuals are available to read on-line or for downloading:
Downloadable documents
- G98 - A primer (pdf - 134Kb)
- G98 Manual Pages (zip file - 663Kb)
Links
Tutorial
G98 Quick Overview
G98 - A Primer (pdf 134Kb)
Getting Coordinates
- Cartesian Coordinates
- Z-matrices
Yeah, but where do I get coordinates?
- Modeling programs
- X-Ray structure
- GaussView
- newzmat
- babel
Quick Overview
The jobs you will typically run include:
- Geometry Optimizations
This is where you use G98 to take your coordinates andlocate a minimim on the potential energy surface of your molecule. You want a minimum generally, because the equilibrium structure for the lowest energy conformation of your molecule is a minimum. Sometimes you do not want the structure to be a minimum because you are studying reactions or structural distortions, but this topic is best dealt with when we discuss frequency calculations. - Frequency Calculations
These types of jobs are run to characterize the stationary points (a minimum is one type of stationary point) found by your geometry optimization. You will often be interested in the spectral data that is generated by these jobs as well. - Single Point Energy Calculations
After you have characterized your stationary point, the fun of calculating desired properties begins. This is the job you wanted to run all along, in most cases. This is where you calculate: - The total energy of the system in question
- Molecular Orbitals
- Charge Distributions
- Dipole Moments
- NMR Sheilding Properties
The files you will use, create and probably delete
- Input files
Commonly named with either the *.com or *.g98 suffixes, these files tell Gaussian what molecule to explore and how to do it. - Log files
So called because the data from the G98 job, the OUTPUT, is stored in a file called *.log - Checkpoint files
These are the files that no human can read. The *.chk files are useful when a job crashes or for retrieving data that would otherwise make the *.log files unweildy. - Formatted Checkpoint files
These files are used to generate orbitals and other high quality graphics. - rwf files
These are the read-write files that are extremely important for larger jobs - they are used to get around the 2 gig memory limit. - PBS files
Observed in the form *.e1#### or *.o1#### they are of absolutely no use to you but appear occassionally.
Getting Coordinates
Cartesian Coordinates -- Ethanol
O 1.325000 0.000000 -1.300000
H 1.325000 0.000000 -0.340000
C 2.672977 0.000000 -1.777344
H 3.177559 0.873652 -1.420931
H 3.177559 -0.873652 -1.420931
H 2.672440 0.000000 -2.847344
Z-matrix -- Ethanol
O
H 1 B1
C 1 B2 2 A1
H 3 B3 1 A2 2 D1
H 3 B4 1 A3 2 D2
H 3 B5 1 A4 2 D3
0.960000
B2 1.430000
B3 1.070000
B4 1.070000
B5 1.070000
A1 109.500000
A2 109.471203
A3 109.471203
A4 109.471231
D1 -60.000007
D2 60.000007
D3 180.000000
Yeah, but where do I get coordinates?
- Modeling Software
There are several software packages that allow you to draw in structures and save your molecules in the appopriate format. Programs in the building that are readily available for this purpose are: - Chem3D
- Maestro
- Spartan
- Sybyl
- Structural Databases
These databases often provide coordinates for structures in pdb format which can easily be converted to cartesian coordinates or a Z-matrix. Commonly accessed databases include may be found on the Computational Chemistry Resource page: http://www/chem.wisc.edu/~lucero/dbases.html - GaussView
Draw in your molecule using the interface provided by Gaussian Inc. The program works pretty much like the standard molecular modeling interfaces, but you can also set up your job, i.e., you get more than just coordinates.
- newzmat
This program is accessed on the command line of either the Research or Graphics Clusters.
The general format is: newzmat -iinputtype -ooutputtype input_file_name.type output_file_name.type
For example: newzmat -ipdb -ocart etoh.pdb etoh.g98 converts an input file called etoh.pdb in pdb format to a file in cartesian coordinates called etoh.g98. Check the G98 User's Manual (there are 2 copies in 9311) for the list of files that may be converted. - babel
The program will take a variety of input files and convert them to a specified output file.
Babel is currently installed on Remsen, but you can download versions for yourself. See the link at: http://www.chem.wisc.edu/~lucero/conversion.htm
Explanation/Actual Lines
Memory specification %mem=10MW Checkpoint file name %chk= Route Line: IMPORTANT # Level of theory/basis set Keywords Mandatory Empty Space Title Put whatever description you want here Mandatory Emptry Space Spin and Multiplicity Spin space Multiplicity Molecular coordinates z matrix or cartesians Mandatory Blank Space end of text buffer ~
Typical File
%mem=10MW %chk=ethanol.chk # B3LYP/6-31G* OPT FREQ B3LYP Geometry Optimization and Frequency Calculation forEthanol 0 1 O 1.325000 0.000000 -1.300000 H 1.325000 0.000000 -0.340000 C 2.672977 0.000000 -1.777344 H 3.177559 0.873652 -1.420931 H 3.177559 -0.873652 -1.420931 H 2.6724 00 -2.847344