[gmx-users] "comm-mode = Angular" gives error

[Jorden Cabal]

Dear Users,
I am trying to perform simulation of a very large and complex system and
which requires me to make the simulation box rectangular cube instead (box
dimension 24.5 nm * 12.5 nm * 12.3 nm) of perfect cuboid in order to
minimize the number of atoms present in the system.

I am facing the problem of interaction between periodic images due to
rotational movement of the macro molecule. I have tried lowering the
*nstcomm* (frequency of removal of center of mass velocity) to 10 and it
seems it might work but the speed become very slow because it also requires
*nstcalcenergy* to 10.

When I use *comm-mode="Angular"* with *comm-grps="system" *it says "*too
many warnings*" and the warning is
*"Removing the rotation around the center of mass in a periodic system,
this can lead to artifacts. Only use this on a single (cluster of)
molecules. This cluster should not cross periodic boundaries*"

*"Although this problem can be ignored using -maxwarn option in the grompp
command. I want to know that if that is the correct thing to do?" *

*Instead, *I have also tried to work this out by changing the* comm-grps=
"Protein" *but then it throws two warnings first being the same as
mentioned above and the second warning says "*Some atoms are not part of
any center of mass motion removal group. This may lead to artifacts. In
most cases one should use one group for the whole system*"

Again this can be ignored using -maxwarn option but is that right to do?
Please suggest me regarding this.
Thank you