Inverse reaction with bond/react command

[Yang_Wang1]

Dear all,
I am now using the bond/react command to do the cross-linking process. But according to the Experimental results, some specified atoms in my system can be bonded or broken. Now I already achieved the bond creation (crosslinking), but I don’t know how to break the previously cross-linked bonds.
In the manual, it is said just reverse the pre- and post-molecule templates, but I tried it still only allows the bond creations, no bonds breaking. Are there any suggestions?

molecule mol1 pre-molecule.data
molecule mol2 post-molecule.data
fix rxns all bond/react stabilization yes statted_grp .03 reset_mol_ids yes &
react rxn1_stp1 all 1 0 5 mol1 mol2 automap.data prob 0.2 237827 &
react rxn1_stp2 all 1 0 5 mol2 mol1 automap.data prob 0.8 231273

fix 1 statted_grp_REACT npt temp 300 300 100 iso 1 100 1000 drag 2

Yang
Best

[jrgissing]

[Yang contacted me prior to this post via email. I am posting his files (with his permission) and my response here, for reference]

The issue is that you are using initiator atoms that have a common atom type, and a Rmax that is unnecessarily long for a bond-breaking reaction. Bond/react is finding other atom pairs with type 6 and checking those against the reaction template. It can be helpful to use a more unique atom pair. For example, if you create another map file for the reverse reaction and set the Initiator Atoms to 12 and 13, you will have reverse reactions. Those atoms make up a relatively unique ‘bonding pair’ within the reaction site

Reaction-crosslinking.zip (609.3 KB)