[gmx-users] Membrane protein simulation

[Behnoush Zare]

Dear Yanzi, 
Of course the system charge is 30+ so I have to add 30 Cl- . So I put “nn 30” to the command like this: 
genion -s protein_pope_em.tpr -o protein_pope_ion.pdb -nname CL- -nn 30 -g protein_pope.log 

But it seems only one water has been replaced with Cl-. Do I have to repeat this step for 30 times?!! or something wrong in this command. 
The protein is larger than box in the Z axis. I tried to add more water in the Z axis by genbox but it just added a few water in one side despite it needs more. Could you please tell me what I should do to fill the empty regions of the box with water. What do you mean about the pope may not be suitable for this protein and how do you understand it? 
Thank you very much in advance for your kindness and expertize. 

Best regards, 
Behnoush