I am looking to have end chains of homopolymers react and form bonds via fix bond/create (exact command copied below). However, I am having a problem because the middle of the chain is able to form a third bond and since I set the max amount of bonds to 2, the code exits. To avoid this, I want to be able to reduce monomers able to form new bonds, limiting it to ends of the chain.
I’ve looked at the group function but I cannot find an easy way to group just the “ends” of the polymer (the atoms with the highest and lowest indices for each molecule).
- Is there an group command to do this that I am missing or is there some other command that I need to use?
- Alternatively, how can I use variable to just target atoms that have 2 bonds at the start of the simulation and subtract those from the all group?
fix 1 all bond/create 10 1 2 1.0 1 prob 0.5 12345 iparam 2 1 jparam 2 2
Thanks in advance,
melt.data (7.61 KB)
in.tild.help (2.11 KB)