Hey everyone,
I want to simulate a polymer confined in a cylinder. I define my cylindrical region and use the wall/region command. I get missing atoms error when I do this. Can someone help me?
my command -
fix wall all wall/region cylin_confine lj126 1.0 0.4 0.448984819
fix 1 all nve
fix LD all langevin 1.0 1.0 0.1 ${seed}
timestep 0.001
run 3000000
The error -
ERROR on proc 0: Bond atoms 474 475 missing on proc 0 at step 218732 (…/ntopo_bond_all.cpp:59)
Maybe the “artificial force” you are imposing as you use the “fix wall/region” command is too aggressive (in the sense that the force component coming from it is sufficiently significant to mess up a lot the dynamics of the polymer atoms to the point of setting them unrealistically farther apart than they should be).
Did you try running the simulation with a different parametrization of the lj126 potential? Or do you actually specifically need it to have the parametrization you input?
I want my particles with diameter of 0.8 to be confined in a cylinder of radius 3.5. I decided to create a cylindrical region of radius 3.9 and used these parameters to ensure the center of my particles always stay in a cylindrical region of 3.5. Is there any other better way to go about this?
Try a gentler wall force function, like harmonic instead of lj126.