[gmx-users] Re: My system is non-zero charge

[Yinghong]

Dear David:
What I simulated is sugar system, which has no termini. And, the corresponding residue topology is [GLCA] (alpha-glucose).

I also know what you mean, but according to the definition of [GLCA], maybe I could not make the total charge in the system be zero.
Or, other factors are not being considered? What is your suggestion to this case?

Thanks very much!

On Sat, 2004-06-05 at 08:13, Yinghong wrote:
> Hi, dear all:
> 
> I have a system which have non-zero charges, normally, we need to add
> counterions (Na or Cl) to neutralize the whole system.
> 
>  
> 
> However, in my system, when I run "grompp", non-integral charges (e.g.
> 1.50e+00) are detected, so under this case, my system 
> 
> could not keep neutral even if corresponding ions are added.
> 
>  

then you have a topology problem in your protein.

> 
> What should I do with this kind of problem?
> 
> Thanks a lot!
> 
>  
> 
> Regards
> 
> Yinghong
> 
> Hongkong University
> 
> 
> 
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-- 
David.
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