[lammps-users] Build molecule template

Dear lammps users,

Do you have any suggestion for the best way to generate lammps data file and molecule template file when a bond between two specific atom ID is created? The purpose is to use this data file as post-reacted in bond/react.


Hi musa,

You can use topotools, atomsk to create Lammps data. By the way, how do you created a bond between two atoms? Di you used any software for that?

Thank you.


I am asking about method of building post reacted file for bond/react.

At the moment, there is no tool that writes out molecule templates directly, that I know of. However, molecule templates are rather similar to data files. So, whichever molecule editor you used to create your system and/or the pre-reaction file, you could add the bond and then print out a post-reaction data file. Let me know if that helps.


Thanks, Jacob and Will,

I found a more efficient way and write it here for those read this mail in the future:

1- First I tried to create the bonding between two specified atoms IDs with fix bond/create. Bond/create really works great for a small number of atoms and also when atom IDs that are specified to be bonded are unique (not repeated several times in the system)
2- Write data after bond/create
3- The new file can be edited and used as a molecule template for bond/react

One thing to keep in mind with this approach is that fix bond/create will only create a new bond with the specified type. Fix bond/create will not account for the new angles, dihedrals, or impropers that exist due to the new bond.