Mixing Special Bond Types

Hi All,

I am preforming self-diffusivity calculations of IPA in the metal-organic framework (MOF) UiO-66, using LAMMPS (Version: May 31st 2019). My MOF potential uses the DREIDING convention for special bonds while my IPA potential is using the CHARMM convention. Does LAMMPS allow for this? I have also erroneously preformed calculations using the CHARMM convention for both IPA and the MOF. My concern is that the diffusion coefficients do not statistically differ between using all CHARMM special bonds and using DREIDING for UiO-66 special bonds and CHARMM for IPA. While this may be correct, based on previous calculations it seems unlikely. As of now, I am using the following commands in an effort to achieve this.

special_bonds dreiding
read_data data.UiO-66 extra/atom/types 5 extra/bond/types 4 extra/angle/types 4 extra/dihedral/types 2

special_bonds charmm
Followed by a set of commands for inserting IPA into the system

I guess my question is best simplified to the following. Does using sequential special_bonds types override the previous special_bonds type? If unsure, is there a good way to preform a sanity check to see that IPA molecules in my system are using CHARMM special bonds and UiO-66 is using DREIDING?

Jacob Wardzala

Your questions are all answered in the LAMMPS manual:
a) the behavior of using the special_bonds command multiple times is discussed in its manual page. your specific question is answered in the second “Note”.
b) the way to apply different special_bonds settings for different force fields is discussed in the documentation for pair_style hybrid. it requires using pair style hybrid since different force fields tend to require different pair styles and then pair_modify to apply the per-substyle special bond settings.