[gmx-users] Re: System has non-zero total charge: 2.570000e+00
tsjerkw at gmail.com
Sun Sep 13 10:06:59 CEST 2009
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
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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