Dear LAMMPS users,
I am trying to simulate a system containing several proteins. I considered my proteins as rigid bodies with interacting patches. Each protein has several patches. I want to control the system so that once two patches are in contact (interacting), no other patches can interact with those anymore, in this way, I will avoid forming unwanted aggregations. I thought I could use bond/create and bond/break for my purpose. So, I added these lines to the input file:
read_data data.start extra/bond/types 1 extra/special/per/atom 1 extra/bond/per/atom 1
bond_style morse
bond_coeff 1 1 10 0.006 #LJ units: Rmin is 0.125 nm
special_bonds lj 0 1 1
fix MAKE22 INTERFACE1 bond/create 10 2 2 0.035 1 prob 1 7456786 iparam 1 2 jparam 1 2
fix BREAK22 INTERFACE1 bond/break 10 1 1.0
But, it doesn’t work as I expected. And I still see, for example, tree patches interacting together at the same time. The other option I found in the documentation is fix bond/react command. But I am even not sure how to use it. Does it make any sense for LAMMPS to recognize that two patches are in contact and ignore them for extra interaction? Any suggestions?
LAMMPS (17 Apr 2024)
Thanks!
Mehr