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

[Justin A. Lemkul]

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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