I would like to simulate a system including 200 molecules constrained by rigid body, as well as 200 molecules without rigid body.
There is a bond connection between each molecule with rigid body and each molecule without rigid body.
I use molecule option in the fix rigid command.
But when I did the energy minimization, I found the relative positions of the particles within one rigid body were changed, especially the particle connected by the molecule without rigid body via bond connection moved a little further.
I tried fix rigid and fix rigid/small, which gave same results.
I am wondering whether it is possible to set up the system like this.
I would like to simulate a system including 200 molecules constrained by
rigid body, as well as 200 molecules without rigid body.
There is a bond connection between each molecule with rigid body and each
molecule without rigid body.
I use molecule option in the fix rigid command.
But when I did the energy minimization, I found the relative positions of
the particles within one rigid body were changed, especially the particle
connected by the molecule without rigid body via bond connection moved a
little further.
I tried fix rigid and fix rigid/small, which gave same results.
as stated in the documentation, none of the rigid fixes are invoked during
energy minimization.
propagation of rigid bodies during energy minimization is non-trivial. you
also have to consider complications due to jamming.
you could try simulated annealing instead (using fix viscous and fix nve),
but jamming is an intrinsic issue for all but the smallest objects.