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

[Vitaly V. Chaban]

In a word, do you use a respectable FF or a instantly made one? :)

~ Vitaly

On Sun, Sep 13, 2009 at 11:06 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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