G03

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You MUST use the "p" keyword for extra-print in all your calculations.

This is an essential requirement to use afterwards the Chemical Repository, where you will need to save your data.

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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 questions & answers

Issues related to the output

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

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, 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.