Recently I wanted to simulate a solid system with a region of atoms fixed. I'm wondering if I want to use NVT to control the system temperature at 300K, should I include the fixed atoms as well? If I exclude the fixed atoms, will they be counted in the force calculations? Thanks!

fix NVT all nvt temp 300 300 0.01
OR
fix NVT mobile nvt temp 300 300 0.01

Recently I wanted to simulate a solid system with a region of atoms
fixed. I'm wondering if I want to use NVT to control the system
temperature at 300K, should I include the fixed atoms as well? If I

better to not include the non-moving atoms.

exclude the fixed atoms, will they be counted in the force calculations?

yes, they will be included in the force calculations.

Thanks for your reply! Just want to make sure, if I use NVE and exclude the
fixed atoms, will they be counted in the force calculations? Thanks again!

you have to be more specific in what you mean by "exclude".

in general, when a force calculation is requested, all forces
that act on the group of atoms selected for time integration
are calculated with two special considerations:

- if you use r-respa, different force contributions are (re-)
computed according to their respa level

- the non-bonded force calculation is based on neighbor lists.
any manipulation of these - either via direct exclusion or
special bonds scaling factors - reflect on which pairs are
considered for the force computation.

if you have doubts about this, i recommend to build some
tiny test systems and write all positions, velocities, and forces
for a few steps and then manually check if the result is what
you expect. depending on how complex your input is, it may
be impossible to describe what is happening in general terms.