[gmx-users] weird output from simultions of a protein between two sheets

[Zuzana Benkova]

Dear Gromacs users,

I want to simulate a protein between two graphene sheets separated by 21 nm. The system is solvated and placed in the cell of dimensions 17.09360  17.18200  25.00000. 
The energy minimzation of this system with position restrain applied to protein and frozen carbon atoms ran OK.
I continued with short simulations in an NVT ensemble with position restrains applied to protein. My output coordinates for all atoms of the systems were integers. Small fragment of a selected frame of the output is as follows

    1GRA     C1    1    0    0    0
    1GRA     C2    2    0    0    0
    1GRA     C3    3    0    0    0
    1GRA     C4    4    0    0    0
    2GRA     C1    5    0    0    0
    2GRA     C2    6    0    1    0
    2GRA     C3    7    0    1    0
    2GRA     C4    8    0    1    0
    3GRA     C1    9    0    1    0
    3GRA     C2   10    0    1    0
    3GRA     C3   11    0    1    0
    3GRA     C4   12    0    1    0

my mdp parameters are as follows

integrator               = md
tinit                    = 0
dt                       = 0.001  
nsteps                   = 100  
comm-mode                = None
nstcomm                  = 0
comm-grps                =
freezegrps               = Gra1 Gra2
freezedim                = Y Y Y Y Y Y
energygrps               = Gra1 Gra2 Protein SOL NA
;energygrp-excl           = Gra1 Gra1 Gra2 Gra2 Gra1 Gra2
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 1
nstcalcenergy            = 1
nstenergy                = 1
nstxout-compressed       = 1   
compressed-x-precision   = 1  
pbc                      = xyz
periodic_molecules       = yes
cutoff-scheme            = Verlet
nstlist                  = 10
ns_type                  = grid
verlet-buffer-tolerance  = 0.005
rlist                    = 1.4   ;ignored with Verlet
coulombtype              = PME   
coulomb-modifier         = None
rcoulomb-switch          = 1.1
rcoulomb                 = 1.3
vdw-type                 = Cut-off
vdw-modifier             = Force-switch
rvdw_switch              = 1.0
rvdw                     = 1.3
DispCorr                 = EnerPres 
fourierspacing           = 0.12  
pme-order                = 4
ewald-rtol               = 1e-05  
ewald-geometry           = 3d  
Tcoupl                   = V-rescale    
nsttcouple               = -1  
tc-grps                  = Protein  SOL_NA  Gra1_Gra2
tau-t                    = 0.1  0.1  0.1
ref-t                    = 310  310  310
Pcoupl                   = no 


I have to note that I got the same output with no position restraints on protein.

Do you have any idea what the problem is? 

Thank you in advance.

Greetings

Zuzana