From: Ashar Malik (asharjm_at_gmail.com)
Date: Sun Aug 06 2017 - 22:41:58 CDT

Your changes are memory/OS dependant. Did you create the other file and see
the 0.0 on another machine? Go back to that previous file creator machine
and have a look at that value their again. Precision is impacted by
numerous factors.

Here is a slide (i just googled it - not mine) to get you started on
floating points.
https://image.slidesharecdn.com/chapter03-arithmeticforcomputers-131229123215-phpapp01/95/chapter-03-arithmetic-for-computers-54-638.jpg?cb=1388320440

On Mon, Aug 7, 2017 at 2:30 PM, <t.shivam_at_iitg.ernet.in> wrote:

>
>
> > On Sun, Aug 6, 2017 at 10:51 AM, <t.shivam_at_iitg.ernet.in> wrote:
> >
> >> Dear vmd users,
> >>
> >> I have a protein solvated in a water box whose net charge is
> >> 7.999999954365194, so when i am using autoionize to neutralize my system
> >> it is showing a charge of -4.563480615615845e-8, i also tried to add 8
> >> chlorine ions instead of going for neutralize option (anyway its more or
> >> less the same thing), so please kindly help me with this problem.
> >>
> >
> > ​there is no problem with autoionize. the problem is between your chair
> > and
> > your computer.​ you are doing floating point math here​​, so -4.5e-8
> > is
> > essentially zero and most certainly zero when rounded to the precision at
> > which partial charges are specified in the CHARMM force field.
> >
> > axel.
>
>
> this might sound funny to you but previously i have solvated my protein in
> a smaller box but the charge of the protein is same (7.999999954365194)so
> at that when i neutralized my system, vmd was showing a perfect zero(0.0),
> so i saved the files of the ionized system, but after that i also created
> a bigger box, and now when i am neutralizing it, it is showing
> -4.563480615615845e-8, and the strangest part is that when i am checking
> my previous system (smaller box showing charge 0.0) it is also showing
> -4.563480615615845e-8,why is that happening?i agree that the value
> -4.563480615615845e-8 is almost zero.
>
> regards
> shivam
> >
> >
> >>
> >> regards
> >> shivam
> >>
> >>
> >
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> > College of Science & Technology, Temple University, Philadelphia PA, USA
> > International Centre for Theoretical Physics, Trieste. Italy.
> >
>
>

-- 
Best,
/A