[gmx-users] question about the output of minimization

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi everybody,
I did a minimization of my structure. But the output seems a bit strange
for me, since my input was the protein with its membrane in a box like
this:
# = box  P = Protein  M=Membrane


#############
#      PPPP #
#     MPPPPM#
#      PPPP #
#           #
#           #
#############

But the output of the minimization looks like this

#############
#        PPPP#
 #M     MPPPP #
  #      PPPP  #
   #            #
    #            #
     ##############

How can that be?
My box was created with:

editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340   4.59470  
5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut


I put solvent in it with:

genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro
2>>logErr 1>>logOut


The mdp file for the minimization looks like this:

define                  = -DPOSRES
integrator              = steep
emtol           = 10
nsteps          = 1500
nstenergy               = 1
energygrps              = System
coulombtype             = PME
rcoulomb                = 0.9
rvdw                    = 0.9
rlist           = 0.9
fourierspacing  = 0.12
pme_order               = 4
ewald_rtol              = 1e-5
pbc                     = xyz


Can you please tell me how I can prevent my box to shift?

Thank you,
Eva