[gmx-users] create a physiological ion concentration

nanyu101 at sina.com nanyu101 at sina.com
Tue Nov 11 03:36:02 CET 2003

Dear gmx-users,
   I want to create a physiological ion concentration for my ion channel+DPPC+water system.I just use genion to replace the water molecule by CA2+ and CL-. After doing this, I have failed to equilibrate the system for the "Fatal error: ci" reason.As my experiences, some atoms crashed. Would you please tell me how to avoid this? 

BTW: before I create the physiological ion concentration, I have put some cations in the right positions of the ion channel and some anions for equilibrium. 

After putting 10 CA2+ and 20 CL- in the ion channel, I have use genion to create a physiological concentration besides the former ions.
  In my system, the concentration of CaCl2 is about 150-200mM and the water molecules in my system is 7000. If I want to create a 200mM concentration, I have to solve 40 CA2+ cations and 80 CL- anions. Because I have already put 10 CA2+ and CL- in the right place of ion channel, there are only 30 CA2+ and 60 CL- remained.

genion -s ion_channel.tpr -np 30 -pname CA2+ -pq 2 -nn 60 -nname CL- -nq -1 -n ion_channel.ndx -o ion_channel.pdb

But I have failed in equilibrating the ion_channel.pdb. Would you please give me some advices? Any comment is appreciated.

Best wishes,

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