[gmx-users] Help in a thermalization

[Graziele Bortolini]

I do it too, my .mdp file now is like :
-----
cpp = /lib/cpp
integrator = md
dt = 0.001
nsteps = 500000
nstcomm = 1
comm-mode = angular
nstxout = 0
nstvout = 0
nstlog = 0
nstenergy = 50
nstxtcout = 50
energygrps = PSB
nstlist = 10
ns_type = grid
rlist = 0
coulombtype = Cut-off
optimize_fft = yes
rcoulomb = 0
vdwtype = shift
rvdw = 0
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 = no
------
but I receive another errors messages:


ERROR 1 [file teste2.mdp]:
  With Verlet lists only full pbc or pbc=xy with walls is supported

ERROR 2 [file teste2.mdp]:
  The box volume is required for calculating rlist from the energy drift
  with verlet-buffer-tolerance > 0. You are using at least one unbounded
  dimension, so no volume can be computed. Either use a finite box, or set
  rlist yourself together with verlet-buffer-tolerance = -1.

ERROR 3 [file teste2.mdp]:
  With switched vdw forces or potentials, rvdw-switch must be < rvdw