[gmx-users] create a physiological ion concentration

[Anton Feenstra]

nanyu101 at sina.com wrote:

> 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.

Is that right, IIRC, water is 70M, i.e. 70000 mM.
May that explain your problems, or is the 7000mM a typo?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
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