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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 6 08:51:31 CEST 2011

```On 6/04/2011 4:42 PM, mohsen ramezanpour 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

See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic

Mark

>
> What is your point of view?
>
>
> 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
>         > 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
>     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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