From: t.shivam_at_iitg.ernet.in
Date: Sun Aug 06 2017 - 23:14:38 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

thanks for the suggestions, but i have used the same machine for the
previous file also.

regards
shivam