[gmx-users] how to create a box for bilayer again!!!

[nanyu101]

Dear gmx-users,
   I just create a cubic box for my bilayer and ion channel.First,I put my channel into bilayer.Second, I try to create a cubic box for my system,but I failed to create a box just as David said.I can't get this box that there are water in z-axis.And I think if I can create this kind of box that the water molecules are in z-axis direction,but after EM,are those water molecules still in z-axis?
  Would you please tell how to generate a box for bilayer that water can just on z axis direction. I can't fix that and when I run EM,the water molecule run into the gap of bilayer and protein.
  So when I run md,the system told me that Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.


  Any comments is recommended.Thanks.

Best wishes,
Xianhui Wu

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