Warnings about using Fix bond/react

LAMMPS LAMMPS Development
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1

Hi everyone,
When I was using Fix bond/react to simulate microtubule crosslinking, there was a warning:
WARNING: Bond/react: Fix bond/react failed because MAXGUESS set too small. ask developer for info (…/fix_bond_react.cpp:1690)
This warning and the MAXGUESS parameter are not found in the manual,I would like to know the reason for this warning and the solution.
This is my template and model：

1
11600×1200 199 KB

2
21600×1200 88.5 KB

As you can see here, the two blue atoms are the ones that are supposed to be cross-linked, and the other picture is the pre-template

Thank you！

2

Why bother with fix bond/react? Why not just use the create_bonds command — LAMMPS documentation?

3

Thanks for your answer, because I want to simulate dynamic crosslinking, and this is just a simplified test model.

4

I tested it again with the template file generated by Auto Mapper, and the warning still appeared.
WARNING: Fix bond/react: Fix bond/react failed because MAXGUESS set too small. ask developer for info (src/REACTION/fix_bond_react.cpp:1737)
The MAXGUESS parameter is not found in the manual.I hope someone can help me answer my question.

5

I am not the developer of the Reacter method, but his code is clear enough for me to make an educated guess:

MAXGUESS is a hard-coded parameter controlling how many times LAMMPS tries to guess a suitable pose for superimposing the bonded template onto the current system. You can only change it by modifying the source code definition and recompiling.

Your template appears to contain hundreds of particles. If the bond initiation particles are often within reach of each other but the hundreds of particles around them never properly line up – and this is something that can only be checked by trying to line them up, which seems to be fairly expensive – it is no wonder you are running into trouble.

6

Thank you very much for your reply