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

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Wed Apr 6 09:28:33 CEST 2011

```Thank you.

On Wed, Apr 6, 2011 at 11:52 AM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> On 06/04/11, *mohsen ramezanpour * <ramezanpour.mohsen at gmail.com> wrote:
>
> 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.
>
>
> Read the other link I provided. 3.000003e00 indicates integer charge. One
> neutralizes it with a set of ions that have a net charge of -3.
>
> Mark
>
>
> 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
>>
>>
>>
>>
>> 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
>>>
>>> What is your point of view?
>>>
>>>
>>>
>>> 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.
>>>>>  >
>>>>> 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
>>>>  If everything looks correct, then the difference is likely a consequence of
>>>> floating-point math and nothing more.
>>>>
>>>> -Justin
>>>>
>>>>
>>>>   Thank you,
>>>>>
>>>>>  Hyun
>>>>>
>>>>>  >
>>>>>  > Mark
>>>>>  > --
>>>>>  > gmx-users mailing list gmx-users at gromacs.org
>>>>>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>  > Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>>  > Please don't post (un)subscribe requests to the list. Use the
>>>>>  > www interface or send it to gmx-users-request at gromacs.org.
>>>>>  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>>
>>>>  --
>>>> ========================================
>>>>
>>>> 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
>>>>
>>>> ========================================
>>>>
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>
>>>
>>>
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.