Issue with Bond Formation between Two Atoms in a Molecular Template

LAMMPS LAMMPS General Discussion
1

Hi everyone,

I’m currently working on constructing a molecular template and I’m having trouble with bond formation between two of the atoms. The output file shows that the reaction is taking place, however, the final structure does not seem to have formed the expected new bond.

Can anyone provide insight into why this might be happening? Any suggestions for troubleshooting would be greatly appreciated.

Thank you!
Here is my input file：in.gro2lam
Input structure:data.gro2lam
Template file: rxn1_stp1_map, rxn1_stp1_reacted.data_template, rxn1_stp1_unreacted.data_template
Output files: log.lammps
Output track file: dump.deposit.atom
Final structure file: data.output
template_files.zip (2.0 MB)

2

The problem here is that you don’t have enough atoms in your reaction templates. Because your system includes dihedrals/impropers, you should include atoms at least three bonds away from reacting atoms. Typically these types of templates would throw an error, but you are slipping through the error checks because none of your atom types are changing between the pre- and post reaction template.