[gmx-users] About Counter-ion

[Anton Feenstra]

> Jang Seokyoung wrote:
> 
> Dear GROMACS USERS...
> 
> I need your advice.
> 
> I have -4.00 charge molecule and +1 charge molecule.
> I want to run normal M.D with this two Molecules in one system.
> but, I don't konw whether using Counter-ion or not.

I am not sure either. It also depends on what you want to
look at in your simulations, and on how you want to publish it
(some journals may be more critical to the 'correct' use of
counter-ions). 

> I think three cases.
> 
>  1. using Counter ion ( 4 Na+ and 1 Cl- )
> 
>  2. not using Counter ion ( Total charge -3.00 )
> 
>  3. Adding Hydrogen atom ( to make -OH instead of O-1 , and NH2
> instead of NH+1 )
> 
> Which is more favorate and more stable ?

I am not sure what you mean by your point 3, is it that you
want to change the protonation state of your molecules? That
does not seem like a good idea, this should depend on the 
relevant pKa and pH values for your system. Option 1 is
probably the best, but then you should also use PME electro-
statics. If you don't want that, but want to use cut-offs
instead, I would recommend not to use counter ions (option 2).

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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