Sorry for the delay in responding. Both the compute pressure
and compute stress/atom commands take a temperature compute ID
as an argument. So if you give them an ID for compute temp/com,
it will use velocities for computing stress or pressure which subtract
out the COM of the system. You can do more sophisticated things
with other forms of biasing the velocities. See the Howto 18.104.22.168
doc page for a list of temperature computes which bias in different manners.
The doc pages for compute pressure and compute stress/atom both discuss
how the velocities they use can be biased.