G03: Difference between revisions
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=== Bader's analysis === | === 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 plot to locate critical points, the maps of density, laplacian, ... Prof. Carles Bo is one of the fathers of Xaim. This program can be download for free at | |||
http://www.quimica.urv.es/XAIM/ | |||
== Scripts == | == Scripts == | ||
Revision as of 14:42, 16 October 2009
go back to Main Page, Computational Resources, Chemistry & More, Computational Codes, GAUSSIAN
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 Scratch. The submision script qs adds the lines
%chk=/scratch/filename.chk %nprocs=XX (XX corresponds the type of node (single or quad core) you requested in qs, where "qs 1 (s/n/l) g03 filename.in" -> %nprocs=1, and "qs 1 (q) g03 filename.in" -> %nprocs=4) %nproclinda=XX (XX corresponds to the number of nodes you requested in qs, where "qs 1 l g03 filename.in" will not add the line, but "qs 4 l g03 filename.in" -> %nproclinda=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=.
- Memory: The qs script does not add a line to specify memory usage, which must be done manually with the "%Mem=" command. The single core nodes have 1GB of RAM, and the quads have 4GB (but only 2GB is accessible due to the 32bit version of Gaussian 03 currently compiled).
As a rule you should specify no more than 85% of a node's memory capacity (single=850MB, quad=1950MB) 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
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, BONDI.. which consider hydrogens explicitly.
-2- Use the keyword SPHEREONH = atom number of the hydrogen "bonded" to two atoms.
- Often Gaussian has problems computing the cavity in specific structures, giving an error message like the one below...
AdVTs1: ISph= 3760 is engulfed by JSph= 3762 but Ae( 3760) is not yet zero!
There are two methods to solve this:
-1- Increase the RMIN value used in the calculation. Increasing the RMIN value smooths the surface of the spheres that make the cavity and helps prevent overlapping. The default value in Gaussian 03 is RMIN=0.20, but you can use any value up to 0.40. You should try to keep the new RMIN within 0.1 vs the default, as a larger difference will give errors in the solvation free energy to the 4th decimal place (from 0.05 kcal/mol upwards).
-2- 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.
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 plot to locate critical points, the maps of density, laplacian, ... Prof. Carles Bo is one of the fathers of Xaim. This program can be download for free at
http://www.quimica.urv.es/XAIM/
Scripts