VMD-L Mailing List

From: t.shivam_at_iitg.ernet.in
Date: Sun Aug 06 2017 - 21:30:32 CDT

> 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.
>