[gmx-users] about box for bilayer system

[nanyu101]

Dear gmx-users,
  I have inserted my ion channel into my bilayer.The system's top file has been edited as you showed in your web. Then I did as follows. 
editconf -f bilayer-ion.pdb -o bilayer-ion.gro 
editconf -bt cubic -f bilayer-ion.gro -o bilayer-ion1.gro -c 
genbox -cp bilayer-ion1.gro -cs spc216.gro -p bilayer-ion.top -o bilayer-ion2.gro 
grompp -f em.mdp -c bilayer2-ion.gro -p bilayer-ion.top -o bilayer-ion.tpr 
mdrun -s bilayer-ion.tpr -o bilayer-ion.trr -c bilayer-ionem.gro 
editconf -f bilayer-ionem.gro -o bilayer-ionem.pdb 
Then I use VMD to view my bilayer-ionem.pdb,I found that there are some water molecules in DPPC leaflet.Why? 

After I have EM my system,I try to run dynamics for my system.I just did as follows:
grompp -f mdrun.mdp -c bilayer-ion.gro -p bilayer-ion.top -o bilayer-ion.tpr
mdrun -s bilayer-ion.tpr -o bilayer-ion.trr -c bilayer-ionmd.gro
The system told me as follows.
  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.

Best wishes,
Xianhui Wu
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