How "fix rigid" works?

Dear all,

I have one puzzling question. I thought, generally, if we change the potential coefficients among rigid body’s atoms themselves and keep other the potential coefficients the same , the result shouldn’t be different, because it’s rigid, right?

However, my simulation result told me it’s different. Why?

Here is my part of code. I just change the sigma and epsilon in pair_coeff 5 5 1.0 1.0 2.5 , others are the same. And all atom 5 forms one particle.

pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 1.12246
pair_coeff 2 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
pair_coeff 3 4 1.0 1.0 1.12246
pair_coeff 5 5 1.0 1.0 2.5

group dimers type 3 4
group no_dimers subtract all dimers
group particles type 5

fix nvtnR no_dimers nvt temp ${Tstar} ${Tstar} $(v_dt*10)
fix nvtR dimers rigid/nvt/small molecule temp ${Tstar} ${Tstar} $(v_dt*10)
fix nvtP particles rigid/nvt molecule temp ${Tstar} ${Tstar} $(v_dt*10)
fix P all press/berendsen iso ${press} ${press} $(v_dt50001000) dilate all

I also have one idea that even if I didn’t change other potential parameters, I do change the particle(atom 5) potential energy, so the difference of particles influence total system?

Thanks very much!

Wrong! the atoms in the rigid object also interact with all other atoms. More specifically, they contribute to the pressure of your system and since you apply fix press/berendsen (not a good idea with rigid objects, BTW) it affects every atom.

Please also note, that it is extremely difficult to discuss only a partial input as there may be other parts that contribute.

The potential coefficients of atom 5 with all other atoms are the same. Could the interaction with all other atoms be still same? I just change the interaction among atom 5 itself.

But fix press/berendsen reacts to the pressure contributions from all atoms and scales the cell accordingly. BTW, the dilate all options is pointless for rigid bodies, since the rigid body COM and orientation and the corresponding velocities will be maintained by the rigid fixes and atom positions and velocities generated from those.