Editing GAUSSIAN (section)

== Gaussian related Tips:==
=== 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/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 ===
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 ===

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/