Is it possible for GRRM20 to read the GRRM17 log files and apply additional calculations?

Dear All,

I have performed MC-AFIR calculations on a periodic boundary system (Siesta),

but I am having trouble with the subsequent RePath calculations.

The input files are as attached.

I would appreciate any advice you can give me.

Thank you in advance.

Dear all,

I am using ADDF method with input file like attached.
Is it possible to specify functions like pm6 or pm7 or Hartree Fock instead of B3LYP/6-31g* ?
The intention is that the calculation takes too long and we want to low the calculation level.
I felt that the calculation would not progress just by entering pm6.
I would appreciate it if you could tell me the specific command if possible.
thank you very much.

Please tell me about the derivation of the reaction rate between EQ-UDC and EQ-TS-DDC by RCMC.
I think the RCMC method analyzes the reaction rate between EQ and TS(PT) with TST(Transition State Theory).

However, how is the reaction rate between EQ and UDC (Upward Dissociation Channel) derived?
I don't think TST can be applied between EQ-UDC because it is difficult to determine a clear transition state.

Also, am I correct in understanding that the reaction rate between EQ-TS-DDC (Downward Dissociation Channel) is derived by TST only for the dissociation reaction and not for the association reaction?

Please tell me about the derivation of reaction rates between EQ-UDC and EQ-TS-DDC by RCMC.
Thank you in advance.

Dear all.

I would like to know the reaction rate in the surface reaction after GRRM.

I am concerned that the distribution function may be treated differently for gas phase and surface reactions.
(I think the distribution function is used for Gibbs energy derivation.)

Is the distribution function of GRRM RCMC treated as gas phase reaction in the Slab model?
Or are they adjusted for surface reactions?

If surface reactions are treated with the gas-phase partition function, then
If so, how large is the error?
If you have any benchmarks that show that the error is not significant, we would appreciate it if you could let us know.
Thank you in advance.

I've tried surface SC-AFIR2 search & got reaction network.

I tried RCMC analysis by RCMC1.txt input file.

But, it only gave RCMC1_sim.log_0 file.

RCMC1_sim.log_1 & RCMC1_sim.log_2 files weren't generated.

And RCMC1_EQ_popl.rrm_* files weren't generated, too.

Will you please give me some advice about RCMC1.txt modification ?

Best regards.

I hope to try DS-AFIR with GRRM20-Siesta combination.

It may need GRRM *.com & Siesta *.inp files.

How to prepare Siesta *.inp file ?

Must I prepare *.inp file for the reactant or the product ? (or both?)

Will you please give me some advice ?

Dear Prof Maeda and group members,

I would like to ask a question about MC-AFIR and RePATH job.

I tried to find possible reaction pathways from phenol oxidation with hydroxyl radical using MC-AFIR, but keep getting an error when I tried to do RePATH job. The message is "error... No structure to be refined...". This is the input for MC-AFIR and RePATH are attached.

Then I tried to do the MC-AFIR example from the tutorial and example input from GRRM school test job. However, I still got the same error as my original input.

Is there anything I can do to fix this issue? Thank you in advance.

I am having trouble understanding how to read the RCMC output.

■ Input : RCMC1.txt

■ Output : RCMC1_sim.log_0

1. I got RCMC1_sim.log_0 as output from RCMC1.com (RCMC1.txt), but
　The following block appears frequently in the file.

   *************************************************************************
　Contraction of the reaction path network
　
　 The V-max parameter = 1.66667e-02 / s-1
　 Delta-G-max value = 192.34 / kJ mol-1
　Temperature = 673.15 / K
　*************************************************************************
　What do V-max and Delta-G-max mean and why do they appear repeatedly?
　V-max and Delta-G-max and why they appear repeatedly.

   (Should I select the one from these sections ? or check the state transition ?)

2. Is it correct to assume that the information in "SS to which each EQ contributes the most:" is just replaced by a matrix of 0s and 1s?

3. what is the unit of "Rate constant matrix (SS-n --> SS-m):"?

4. what does "Traffic volume for EQ - ***" mean?

5. 9 SSs are obtained, is it possible to visualize them properly?
　I see five EQs in "Five representative EQs in SS 0:"
　Are there different proportions of the magnitude of each contribution? (is it possible to figure out?)
　SS 0 involves 5 EQs, EQ1, 0, 2, 3, 13, but
　EQ1, 0, 2, and 3 will have nearly the same structure while EQ13 is very different.
　Is it necessary to ascertain the contribution from each EQ in such a case?

I would be very grateful if you could enlighten me.
Thank you in advance.

When I create an input file, the file extension is .xyz, .cif, .pdb, and so on.

How convert from these file extensions to .com and .inp (input file of GRRM20 with SIESTA) ?