Slowing down of majority of atoms

Hello Steve, Alex and all,

I have been using LAMMPS simulation for simulating adsorption of colloidal particles to “sites”. My particles are
‘SPHERE’ type with uniform particle size. the “sites” are also ‘SPHERE’ type particles with a very high (1e12)
density so that they do not move. I use a Yukawa-Colloid style potential for particle-particle and LJ- for site-Particle.
I initially let the particles spread out inside a reservoir-box, and then remove a wall that allows diffusion of particles to the
region where the “sites” are located. I have attached the input file for the system in this mail.

Here is what happens once i open the gates - Some of the particles stick to the sites and are strongly bound there,
but once about 10-15 particles (out of 225) get stuck to the sites, all the other particles in the reservoir-box slow down
drastically (almost like frozen) - while the atoms on the sites keep moving as before though within the influence of the
sites. I do not believe this is realistic and suspect that it is an artifact because of the site atoms. I saw someone
describing a similar situation in this post - - where Steve had
mentioned about part of the atoms freezing and some flying about at high velocity. Is there a possible explanation
for this?

What I think is happening is that, since I am rescaling to a constant temperature, the particles stuck to the sites
acquire a high velocity/vibration and start eating up all the kinetic energy. Please give me your opinion/views.

Thanks and regards,


in.wall3D_42_forsteve (1.69 KB)

You would have to be careful how you calculate temperature if some
particles have huge mass (due to high density) and others do not.

I would probably only try to thermostat the mobile particles, and also
only measure their temperature. You can also just not integrate
the "site" particles and they will never move. So there is no need
to make them very dense/heavy.