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polymerization setting

5 polymerization setting
Shunsuke Mieda June 3, 2020, 9:14 a.m. #105

Dear all

Hello, I'm trying to run GRRM 17 program to examine polymerization reactions including Butadiene.

At first, I have tried to calculate the very simple reaction as below. However, any TS structure has NEVER been generated although GAMMA parameter was very large, SC-AFIR was changed to SC-AFIR2, or the different functionals were used.

To react these molecules, could anyone teach me what options should be tested, or how to set the input file.

Thanks.

S. Mieda

----Input file sample-----------

# SC-AFIR/B3LYP/6-31G

-1 1
C -6.04851 1.08683 -0.12952
C -4.65656 0.67303 -0.47198
C -3.56045 0.80445 0.37107
C -2.26684 0.40808 0.06896
H -6.39564 1.86874 -0.83809
H -4.49975 0.21350 -1.45756
H -3.73818 1.26439 1.35332
H -2.03118 -0.05733 -0.89259
C -7.06260 -0.07494 -0.17775
H -6.60275 -1.00092 0.30256
H -6.06390 1.54725 0.87543
H -1.44681 0.54598 0.77726
H -7.32889 -0.30211 -1.26268
C 3.12328 4.11991 -0.42148
C 1.91711 4.54010 0.00136
C 0.68735 4.38233 -0.75186
C -0.52022 4.79402 -0.32435
H 4.02317 4.26027 0.18117
H 3.24530 3.62228 -1.38871
H 1.82997 5.03655 0.97605
H 0.77488 3.88934 -1.72815
H -0.64143 5.28864 0.64465
H -1.42164 4.64671 -0.92286
H -8.00546 0.21979 0.39125
Options
Add Interaction
GAMMA = 1000
Fragm.1 = 1-13,24
Fragm.2 = 14-23
1 2
END
GauMem = 2000
GauProc = 4

  • Re: polymerization setting
    Kenichiro Saita

    I have tested a SC-AFIR calculation using your sample input; the artificial force was not applied between any fragments because the two moieties were too far away (the input structure (EQ0) had judged as a dissociation channel (DC) structure by the default parameter DownDC=8, and you would be able to see the string "Not to be applied" in the file jobname_EQ_test.rrm.). Therefore, no reaction paths had been computed and no TS structures had also been generated.

    Does the intermolecular distance have a meaning (e.g. experimentally solved structure)? If no, it might be worth to try a MC-AFIR calculation. In addition, I think "Stable=Opt" option is recommended in your case.


    ----- Sample Input for MC-AFIR -----

    # MC-AFIR/B3LYP/6-31G
     
    -1 1
    C -6.04851  1.08683 -0.12952  1
    C -4.65656  0.67303 -0.47198  1
    C -3.56045  0.80445  0.37107  1
    C -2.26684  0.40808  0.06896  1
    H -6.39564  1.86874 -0.83809  1
    H -4.49975  0.21350 -1.45756  1
    H -3.73818  1.26439  1.35332  1
    H -2.03118 -0.05733 -0.89259  1
    C -7.06260 -0.07494 -0.17775  1
    H -6.60275 -1.00092  0.30256  1
    H -6.06390  1.54725  0.87543  1
    H -1.44681  0.54598  0.77726  1
    H -7.32889 -0.30211 -1.26268  1
    C  3.12328  4.11991 -0.42148  2
    C  1.91711  4.54010  0.00136  2
    C  0.68735  4.38233 -0.75186  2
    C -0.52022  4.79402 -0.32435  2
    H  4.02317  4.26027  0.18117  2
    H  3.24530  3.62228 -1.38871  2
    H  1.82997  5.03655  0.97605  2
    H  0.77488  3.88934 -1.72815  2
    H -0.64143  5.28864  0.64465  2
    H -1.42164  4.64671 -0.92286  2
    H -8.00546  0.21979  0.39125  1
    Options
    NFault = 50
    Add Interaction
    GAMMA = 1000
    Fragm.1 = 2-4
    Fragm.2 = 14-17
    1 2
    END
    Stable = Opt
    GauMem = 2000
    GauProc = 4
     

    --------------------

    This is just my comment, and this might not be a solution to your problem...

  • Thank you
    Shunsuke Mieda

    Saita-Sensei

    Thank you for the great advice!

    I'm trying to shorten the distance between two fragments, to use the options, and to generate multi-structires by using MC-AFIR.

    BTW... could you teach me why the fragment ranges were changed? Did the wide ranges have bad influence on the reaction?

     

    Best regards,

    S. Mieda

  • Re: Thank you
    Kenichiro Saita

    In the above sample input for MC-AFIR, only the sp2 carbon atoms are selected for the fragment. It would be a natural choice in terms of the chemical knowledge, but it was not a strong suggestion. In order to make a global search, the wider fragment range would be required, but it would take a long computational time. So, I chose only the sp2 carbon atoms to the fragments as a sample job.

    NOTE: The terms "part" and "fragment" are used in different meanings in GRRM17 program:

    · "Fragment" means the fragment to which the artificial force is applied by the AFIR function.
    · "Part" means a moiety of the system (or a monomer in the molecular cluster). The defined parts to be used for random geometry generation (all parts to be randomly distributed).

    The fragment is not necessarily identical to the part. For details, please see the manual page.
    In the SC-AFIR calculation, the fragments to be automatically defined, so that you do not have to put the lines "Fragm.1 = 1-13,24" and "Fragm.2 = 14-23" into the SC-AFIR input file.

  • Re: polymerization setting
    Kenichiro Saita

    (For your information) this might be an example input file for SC-AFIR local search:

    ----- Sample Input for SC-AFIR -----

    # SC-AFIR/B3LYP/6-31G
     
    -1 1
    C -6.04851  1.08683 -0.12952  1
    C -4.65656  0.67303 -0.47198  1
    C -3.56045  0.80445  0.37107  1
    C -2.26684  0.40808  0.06896  1
    H -6.39564  1.86874 -0.83809  1
    H -4.49975  0.21350 -1.45756  1
    H -3.73818  1.26439  1.35332  1
    H -2.03118 -0.05733 -0.89259  1
    C -7.06260 -0.07494 -0.17775  1
    H -6.60275 -1.00092  0.30256  1
    H -6.06390  1.54725  0.87543  1
    H -1.44681  0.54598  0.77726  1
    H -7.32889 -0.30211 -1.26268  1
    C  3.12328  4.11991 -0.42148  2
    C  1.91711  4.54010  0.00136  2
    C  0.68735  4.38233 -0.75186  2
    C -0.52022  4.79402 -0.32435  2
    H  4.02317  4.26027  0.18117  2
    H  3.24530  3.62228 -1.38871  2
    H  1.82997  5.03655  0.97605  2
    H  0.77488  3.88934 -1.72815  2
    H -0.64143  5.28864  0.64465  2
    H -1.42164  4.64671 -0.92286  2
    H -8.00546  0.21979  0.39125  1
    Options
    NRUN = 1
    Add Interaction
    Target = 2-4,14-17
    GAMMA = 200
    END
    SC = InterOnly
    Stable = Opt
    GauMem = 2000
    GauProc = 4
     

    --------------------

    NRUN is used in order to generate a random initial structure.
    SC = InterOnly limits the number of paths to be computed (artificial force to be applied between different parts only).

    This is just an example. The SC-AFIR has various options, so you may wish to experiment to decide which one fits your needs best.

  • Re: Re: polymerization setting
    Shunsuke Mieda

    Saita-sensei

    Thank you very much for the useful comments.

    I understand the difference between Frangments and Parts (and Targets).

    Especially, SC = InterOnly option seems to be very useful for my calculation. I'm trying to use the other options for SC-AFIR, too.

    If the reaction is carried out, I write the input file here to share the information.

     

    Best regards,

    S. Mieda