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

Hyunsik nammika at hotmail.com
Wed Apr 6 13:53:22 CEST 2011 

hm...
is it possible that there is partial charge because of terminal of zwitterions?
(NH3+ and COO-)

When i tried to make system with terminal of just NH3+ and COO-, there was no partial charge like 5.00.

But when i used zwitterion terminal, that made the 5.05 charge of the system..

it can be happened? Or something weird?

Hyun

2011. 4. 6., 오후 5:00, Erik Marklund 작성:

> mohsen ramezanpour skrev 2011-04-06 09.31:
>> 
>> 
>> 
>> On Wed, Apr 6, 2011 at 11:53 AM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
>> Hi,
>> 
>> No we don't. You can't have fractions of elementary particles in your molecules.
>> 
>> Dear Erik
>> 
>> Yes,You are right.It is obvious .
>> But I wanted to simulate a part of my system.for example a part of my protein!
>> I was wrong,we can't do that 
>>  
> I think there are several examples of that in literature, e.g. by Åqvist and coworkers. But think they use a different approach than just cutting away part of the protein.
> 
> Erik
>> Erik
>> 
>> mohsen ramezanpour skrev 2011-04-06 09.13:
>>> 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
>>>>  > --
>>>>  > gmx-users mailing list gmx-users at gromacs.org
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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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>> 
>> 
>> -- 
>> -----------------------------------------------
>> Erik Marklund, PhD student
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>> phone:    +46 18 471 4537        fax: +46 18 511 755
>> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>> 
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> 
> 
> -- 
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
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