[gmx-users] Re: System has non-zero total charge: 2.570000e+00

[Tsjerk Wassenaar]

Hi,

On Sun, Sep 13, 2009 at 8:55 AM, Vitaly V. Chaban <vvchaban at gmail.com> wrote:
>> before energy minimization step , I performed the preprosessing step using grompp  . However, there’s a note that : System has non-zero total charge: 2.570000e+00 “.
>> why the total charge of system is not an integer?
>
> The charge is too big to be the result of rounding. The first question
> is: what charge (integer) of the system do you expect? May the value
> you report here occur due to the wrong force field you apply?

No. No force field should yield a partial charge for a molecule. It
should always end up integer. Here, either a hand made topoloy was
used, which was not set up properly, or a wrong choice was made
somewhere, probably pertaining to the termini (Zwitter ion in stead of
charged?).

Cheers,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623