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

[mohsen ramezanpour]

Daer Dr.Mark

You are right,But all of them(as I know) have integer charges!
the problem is simullating a system with partial charges.
We absolutely have such systems.

On Wed, Apr 6, 2011 at 11:22 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 6/04/2011 4:45 PM, mohsen ramezanpour wrote:
>
> 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?
>
>
> I suspect every tutorial for simulating proteins in water deals with the
> need for counter-ions, and the technique for generating them.
>
> Mark
>
>
>  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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>>
>>
>
>
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