Hello all,
Currently, I’m interested in trying to run a fairly simple implicit membrane simulation using LAMMPS. Essentially, this would entail applying mild positional restraints to the membrane protein I’m studying, as well as defining a “belt” around the protein with a different dielectric constant to reflect the membrane’s different electrostatic character.
I am already familiar with the various restraining commands in LAMMPS, including fix spring, fix restrain, etc, and I believe I understand how to define a belt region using the corresponding built in command as well. I also see there is an option to change the dielectric constant, which appears to do what I need, however I still have some questions about combining these features:
1.) The page describing the dielectric command is quite terse, and so it seems that once a dielectric is defined, it is applied throughout the entire simulation box by default. As a result, I was wondering if there is a way to combine various geometric commands in LAMMPS to restrict the modified dielectric constant to a roughly cubical subregion of the total simulation box?
2.) Would it be consistent to use the dielectric command if I am also using an implicit solvent force field to account for the water interactions? Or would this be over-correcting? Obviously I can test some of this through direct simulation once I have things set up, but I was wondering if there was any way to have some insight about this a priori.
Thanks,
Tom Allen