Thanks for your reply.
Actually, in my model, I have three primary parts, group A, B and C. A is
considered as a NVT ensemble. Group B is combined with C as a rigid body and
have time integration, but not included in the ensemble. So, I guess I could
not put fixed zero force on B. Otherwise, how can B move along with C?
that sounds very much like a setup that i just discussed with a
colleague over the last days (only that he wanted a different
shape of object to have this kind of interaction).
in my opinion, the best way to implement this would be to write
a "fix". the fix operates on one group (A atoms) and computes its
forces based on the position of C. have a look at, e.g., "fix spring"
with the couple option wich applies a spring force on one group
based on the position of another group.
Certainly, no need to count the interaction between B and C. Regarding the
role of group B, ideally it can be a massless repulsive wall associated with
group C when group C is approaching group A. However, I don't want the force
from group A acting on the wall (group B). Only group A can feel the
repulsive force from the wall so that atoms in A won't penetrate the wall. A
and C have the normal interatomic interaction.
if it is a wall you want, you could look into programming a variation
of "fix wall". that can currently already be moving at constant
velocity, so you'd just compute its position based on the position
of the C atoms. if you only want a repulsive wall, you have choose
the cutoff so that it is in the minimum of the potential.