Help with fix bond/react

LAMMPS LAMMPS General Discussion
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1

I am trying to run coarse-grained simulation of a catalytic bond breaking event. The reaction template involves a fragments of a polymer chain (atoms 1-2-3-4) and a catalytic molecule (5-6). I set atom 1 as the edge atom as it is connected to the rest of the polymer chain. But when I ran the simulations, I kept getting the following error message:
Fix bond/react: Excessive iteration of superimpose algorithm. Please check that all pre-reaction template atoms are linked to an initiator atom, via at least one path that does not involve edge atoms. (src/REACTION/fix_bond_react.cpp:1450

Here I attach my template files:

Before reaction:

molecule template: chain end structures before rxn

    6  atoms
    4  bonds
    0  angles
    0  dihedrals

Coords

    1    19.899810791    12.733695984    18.098842621
    2    18.919700623    13.421165466    17.828743744
    3    18.019700623    14.717165466    17.028743744
    4    17.519700623    15.421165466    16.528743744
    5    12.919700623    13.421165466    17.828743744
    6    14.019700623    13.021165466    17.728743744

Types

    1    1
    2    2
    3    2
    4    7
    5    4
    6    5

Charges

    1    0
    2    0
    3    0
    4    0
    5    0
    6    0

Molecules

    1    1
    2    1
    3    1
    4    1
    5    2
    6    2

Bonds

    1    1    1    2
    2    2    2    3
    3    5    3    4
    4    3    5    6

After reaction:

molecule template: chain end structures after rxn

    6  atoms
    3  bonds
    0  angles
    0  dihedrals

Coords

    1    19.899810791    12.733695984    18.098842621
    2    18.919700623    13.421165466    17.828743744
    3    18.019700623    14.717165466    17.028743744
    4    17.519700623    15.421165466    16.528743744
    5    12.919700623    13.421165466    17.828743744
    6    14.019700623    13.021165466    17.728743744

Types

    1    1
    2    2
    3    2
    4    8
    5    4
    6    5

Charges

    1    0
    2    0
    3    0
    4    0
    5    0
    6    0

Molecules

    1    1
    2    1
    3    1
    4    3
    5    2
    6    2

Bonds

    1    1    1    2
    2    2    2    3
    3    3    5    6

Map file:

map file

1 edgeIDs
6 equivalences

InitiatorIDs

4
5

EdgeIDs

1

Equivalences

1       1
2       2
3       3
4       4
5       5
6       6

From how I understand the algorithm, all the atoms should be connected to the initiator through a path that does not involve the edge atom, except for the edge atom itself. So I don’t understand why I am seeing this error. Any help is appreciated!

2

There was some version of this post that was deleted, do you still need help? If so, please post all the files necessary (including input file, data file) to run a short simulation to reproduce your issue.

3

Thank you for your response! Since I am a new user, the group does not allow me to post any files along with the reply. Is there an alternative way to share the files?

4

Yes, you can provide links to other file-hosting services.

5

Thank you! Please find the files at the following link: Dropbox
The runs include more reactions than I have shared above. The activation step and depolymerization steps have been tested separately without any issues. The error only popped up when I added the chain end cyclic structure detachment step, specifically the reaction with “Cyclic_detatch_middle_map” in the filename, and rxn4 in the bond/react fix in the input file.
BTW I am using LAMMPS (12 Jun 2025) version. Thank you so much for your help!

6

The input file you provided does not run. Can you provide a working example? It would also be very helpful to provide a much smaller example that reproduces your issue.

7

Sorry I forgot to provide a script to run with the input script. Please see the test.sh script that I just added to the dropbox folder which includes all the variables. It is a bit hard to create a smaller system at this point, since the initial condition was generated through a different equilibrium run. If this does not work, I can try to initiate a smaller system and update you with the new data file. Thank you so much for your help!

8

It looks like the issue is a typo in the input script for rxn5: you switched your pre- and post-reaction templates.

9

Ah thanks for pointing it out!! I did a test run and now it’s working fine. I thought it’s the problem with rxn4. Thank you for your help!