[gmx-users] Inconsistent shifts after switching form 4.5.7 to 5.0.4 version

[Mikhail Stukan]

Dear Gromacs users,

Good someone give me a hit about the following issue. I am running a system which contains few periodic molecules (graphene sheets). Everything was running fine when the simulations were performed using group cut-off scheme and GROMACS 4.5.7. However, when I tried to transfer the same system to 5.0.4 version and switch from group to Verlet scheme the run crashed with the following error:
"There were 80 inconsistent shifts. Check your topology"

No changes in topology files were performed. The difference in MDP files between two cases is shown below. Am I doing something obviously wrong?

Many thanks in advance,
Mikhail

MDP-file for 5.0.4 (error about inconsistent shifts )

pbc                 =  xyz              ; periodic boundary conditions
cutoff-scheme       =  Verlet
verlet-buffer-drift =  0.005
;================== Electrostatics
coulombtype         =  PME
rcoulomb            =  1.2              ; cut-off for coulomb
;================== Van der Waals
vdw-type            =  switch
rvdw_switch         =  1.0
rvdw                =  1.2              ; cut-off for vdw
;================== EWALD/PME/PPPM parameters
fourierspacing      =  0.12
pme_order           =  6
ewald_rtol          =  1e-06
epsilon_surface     =  0
optimize_fft        =  yes              ; perform FFT optimization at start

old MDP-file for 4.5.7 (running without any trouble)

pbc                 =  xyz              ; periodic boundary conditions
periodic-molecules  =  yes              ; in the system present periodic molecules
rlist               =  1.5              ; cut-off for ns
;================== Electrostatics
coulombtype         =  PME
rcoulomb            =  1.5              ; cut-off for coulomb
;================== Van der Waals
vdw-type            =  switch
rvdw_switch         =  1.0
rvdw                =  1.2              ; cut-off for vdw
;================== EWALD/PME/PPPM parameters
fourierspacing      =  0.12
pme_order           =  6
ewald_rtol          =  1e-06
epsilon_surface     =  0
optimize_fft        =  yes              ; perform FFT optimization at start