AFIRサンプル

IRC Calculation

1 IRC Calculation
Cristina Nevado Sept. 16, 2019, 8:32 p.m. #83

I am interested to run IRC calculations with GRRM of some transition states that I obtained with Gaussian.

2 log files are generated in the calculation: name.log and name_GauJOB.log.

I run one file getting normal termination but when I open the file name_GauJOB.log in GaussView I cannot see the expected movement of the molecule (reverse or forward).

Maybe I did not indicate in the file the correct parameters. 

My file:

 # IRC/b3lyp/GenECP

0 1

COORDINATES

Options
GauMem = 200
GauProc = 8
NoBondRearrange
Bond Condition
12 75 < 2.06
Add Interaction
Fragm.1=1-40
Fragm.2=41-75
1 2

GAMMA = 200

END
GauInpB
C H N O F Si
6-31g**
****

Au 0
SDD
END

 In this example, I indicate as Bond Condition 12 75: I am working with transition states:

 Here, do I have to indicate the numbers of the 2 atoms involved in the formation of the new bond, right?

  1. When I open the log file of my transition state (obtanied in Gaussian) in gaussview I see the movement of the atoms when I select the option Vibrations. Which is the distance that I have to indicate for the calculation in GRRM?. Is the distance that I have before to select vibrations? The distance that I have to indicate is the difference between the distance of these atoms in the product and the precursor? or between the transition state and the product?
  2. Do I indicate > or < based on what?

 Thank you very much in advance for your kind help

 

  • Re: IRC Calculation
    Kenichiro Saita

    The GRRM17 program uses Gaussian program to only compute single point calculation, and the file name_GauJOB.log is the Gaussian log file of the last step of your calculation. In this case, it would correspond to the freq calculation log file at the minimum point of the backward IRC path, so that you cannot see the IRC path information in the file name_GauJOB.log with GaussView. The IRC information is stored in the file name.log. To visualize the structure in IRC path computed by GRRM17 with GaussView, you need to plot the corresponding structure and energy separately from the file name.log.

    In the "Bond Condition ... END" option, "12 75 < 2.06" means "the distance between atoms 12 and 75 to be less than or equal to 2.06 angstroms". This bond condition will be appled to the SC-AFIR search, but not to the IRC path calculation. Do not confuse this option with the IRC=Phase=(N1,N2 [,N3 [,N4]]) option in Gaussian. In GRRM17, an IRC calculation always computes forward and backward IRC paths.

    The options "NoBondRearrange", "Bond Condition ... END", and "Add Interaction ... END" have no effect on the IRC calculation, because "IRC" keyword just performs the IRC path calculation. Such options are effective in the "SC-AFIR" calculation. In SC-AFIR, the "Bond Condition ... END" option cannot be used simultaniously with the "NoBondRearrange" option (the latter keyword in the input file is only effective).

    You may need to add the basis to the valence part of Au:

    GauInpB
    C H N O F Si 0
    6-31g**
    ****
    Au 0
    SDD
    ****

    Au 0
    SDD
    END

  • Re: IRC Calculation
    afiradmin

    This issue seems to be solved by the above comment. (However, you can still add comments to this thread.)