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

[Mark Abraham]

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 <mailto: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
>     <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>         김현식 wrote:
>
>
>
>             > Date: Tue, 5 Apr 2011 23:43:19 +1000
>             > From: Mark.Abraham at anu.edu.au
>             <mailto:Mark.Abraham at anu.edu.au>
>             > To: gmx-users at gromacs.org <mailto: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 <http://vt.edu> | (540) 231-9080
>         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>         ========================================
>
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