[gmx-users] Help in a thermalization

[Graziele Bortolini]

When I tried to do a thermalization for a PSB molecule (it has 66 atoms),
in vacuum, the molecule rotate around the center of mass. This's my .mdp
file:
-------------------
cpp = /lib/cpp
integrator = md
dt = 0.001
nsteps = 500000
nstcomm = 1
nstxout = 0
nstvout = 0
nstlog = 0
nstenergy = 50
nstxtcout = 50
energygrps = PSB
nstlist = 10
ns_type = grid
rlist = 0.4
coulombtype = Cut-off
optimize_fft = yes
rcoulomb = 0.8
vdwtype = shift
rvdw = 0.8
tcoupl = berendsen
tc_grps = system
ref_t = 300.0
tau_t = 0.1
pcoupl = berendsen
ref_p = 1.000
compressibility = 4.5e-5
tau_p = 1.0
pcoupltype = isotropic
gen_vel = yes
gen_temp = 300.0
pbc = xyz
-------------------
So, I tried to put the "comm-mode = angular", it supposedly remove center
of mass translation and rotation. But when I do it I receive the following
message:

"WARNING 1 :
  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."

What I'm doing wrong?
-- 
Att.
G. Bortolini