[gmx-users] Re: My system is non-zero charge
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jun 4 16:49:40 CEST 2004
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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