Dear all,
UPDATE: Bug fixed! I need to remove the H linked to edge atom, according to “All pre-reaction template atoms should be linked to an initiator atom, via at least one path that does not involve edge atoms.”
I tried to test my script using the tiny_nylon example, but with GAFF forcefield.
I have a problem with my template and map files. It told me to 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.
I have checked my template and map files, it does have a path from edge atom to initiator atom. here are the files and commands I used:
LAMMPS version: LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-566-g224468d946)
system.data (8.0 KB)
nylon.in (1.4 KB)
rxn1_stp1_reacted.mol (3.8 KB)
rxn1_stp1_unreacted.mol (3.3 KB)
rxn1_stp1.map (231 Bytes)
rxn1_stp1_reacted_mol.data (4.5 KB)
rxn1_stp1_unreacted_mol.data (3.9 KB)
NOTE: *_mol.data is for molecule template visualization and debug.
UPDATE1: In the pre-reaction template, should both parts of the residues be assigned the same molid? I tried both approaches (assigning the same molid in the Molecules section), but both resulted in the same error.
UPDATE2: molid seems not effect polymerization.
molecule mol1 rxn1_stp1_unreacted.mol
molecule mol2 rxn1_stp1_reacted.mol
molecule mol3 rxn1_stp2_reacted.mol
fix myrxns all bond/react stabilization yes statted_grp .01 &
react rxn1 all 1 0.0 4.0 mol1 mol2 rxn1_stp1.map
# react rxn2 all 1 0.0 5.0 mol2 mol3 rxn1_stp2.map
# just try the first step
PS: should I separate step 2 into two steps? Here are my second-step files(I haven’t test it, because the first step failed):
rxn1_stp2.map (231 Bytes)
rxn1_stp2_reacted.mol (3.4 KB)
rxn1_stp2_reacted_mol.data (4.1 KB)