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

[David van der Spoel]

On Sat, 2004-06-05 at 08:31, Yinghong wrote:
> 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?
check the chemistry. you probably need a proton somewhere...
> 
>  
> 
> 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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