[gmx-users] How to remove charge of 5e-2 ??

[mohsen ramezanpour]

Dear Dr.Justin

I had the same problem.
I modified the charges and charge groupsin the  topology of a drug.the net
charge of it is zero(I am sure)
though,when I used pdb2gmx it resulted a NOTE like the following:

NOTE:The system has non-zero total charge: 3.000003e00
I continued simulation and ignored it!
Because:
1- I checked my protein.top and qtot was 3
2-the net charge of my drug was 0
3-Besides,all charges have 3 digit precision,How can it have 0.000003
additional charge?!

What is your point of view?
Thanks in advance for your reply


On Wed, Apr 6, 2011 at 3:40 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 김현식 wrote:
>
>>
>>
>>  > Date: Tue, 5 Apr 2011 23:43:19 +1000
>>  > From: Mark.Abraham at anu.edu.au
>>  > To: gmx-users at gromacs.org
>>  > Subject: Re: [gmx-users] How to remove charge of 5e-2 ??
>>  >
>>  > On 5/04/2011 11:17 PM, Hyunsik wrote:
>>  > > Dear experts,
>>  > >
>>  > > Hi,
>>  > >
>>  > > When prepare a system, the system had +5.5. So I add 5 CL- ion to
>> neutralize.
>>  > >
>>  > > But as you know, the Cl charge is -1 and there still is 5e-2. how can
>> i remove that.
>>  >
>>  > Your statements are inconsistent. If you had 5.5 charge and added five
>>  > chloride ions, you could not end up with 0.05.
>>
>>  oh.. I have mistaken.. I had 5.005 of the system charge.
>>   So even if added five choride ions, the system charge is not zero. there
>> was 0.005
>>
>>  that is partial charge??  If like that, topology is broken or something
>> wrong? abnormal??
>>
>>
>
> Maybe, maybe not.  Rounding errors could account for this difference,
> especially if your system is very large.  Still, you should inspect your
> topology/topologies for inconsistencies.  If pdb2gmx created the topology,
> keep an eye on the "qtot" column for a running total of the charge.  If
> you've made or adjusted any topologies on your own, double-check your work.
>  If everything looks correct, then the difference is likely a consequence of
> floating-point math and nothing more.
>
> -Justin
>
>
>   Thank you,
>>
>>  Hyun
>>
>>  >
>>  > Mark
>>  > --
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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