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

[mohsen ramezanpour]

Dear Dr.Justin

What can we do (how can neutralize system) if the total charge of our system
was not integer?
I think  there is not any solution and we have to simulate a charged system
not a neutral.
Am I right?
Thanks in advance

On Wed, Apr 6, 2011 at 11:12 AM, mohsen ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> 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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