[gmx-users] problem with system neutralization

[Justin A. Lemkul]

As an aside, I have found that using the -neutral flag of genion only works in 
conjunction with a specified -conc.  This is somewhat counterintuitive and not 
explained by the documentation.  Is this perhaps a bug?

-Justin

Pawan Kumar wrote:
> Hello,
> 
> Greetings from Pawan.
> Giving the command and the options being used will be much better to 
> give any further probable suggestions.
> Just using " -np 4 " wont solve the problem as such. You should specify 
> the " -pname " option also. You can use NA+ ions to neutralize the 
> system as its having negative charge. And when specifying the -np or -nn 
> option u need not use -neural option.
> 
> Regards,
> Pawan
> 
> 
> 
> On Fri, May 22, 2009 at 4:30 PM, Stefano Meliga <smeliga at gmail.com 
> <mailto:smeliga at gmail.com>> wrote:
> 
>     Thanks Pawan,
> 
>     I added 4 positive ions as you suggested but the system total charge
>     reported in genion.log is still -4!
> 
>     Why?
> 
>     Cheers,
> 
>     Stefano
> 
> 
>     Pawan Kumar ha scritto:
> 
>         Hello,
> 
>         Greetings from Pawan.
>         -np is a parameter used to add the nmber of positive ions.
>         when u have -4 negative charge u should give -np 4.
>         -np with -pname will be more appropriate.
>         see through this website for the proper usage of genion options.
>         http://www.gromacs.org/documentation/reference_3.3/online/genion.html
> 
>         Regards,
>         Pawan
>         On Fri, May 22, 2009 at 3:20 PM, Stefano Meliga
>         <smeliga at gmail.com <mailto:smeliga at gmail.com>
>         <mailto:smeliga at gmail.com <mailto:smeliga at gmail.com>>> wrote:
> 
>            Dear all,
> 
>            As the on-screen output of grompp says, my system has non-zero
>            total charge = -4.000
> 
>            Thus, I'm trying to neutralize the system using genion with this
>            command line:
> 
>            genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
>            4AKEallHsol_pre.top -neutral
> 
>            The problem is that the on-screen output says:
> 
>            "No ions to add and no potential to calculate"
>            as the system was already neutral, I guess.
> 
>            I then tryied with the command line:
> 
>            genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
>            4AKEallHsol_pre.top -neutral -np 50 -g
> 
>            Ions are added to the SOL group but the total charge remains -4,
>            as the log file says.
> 
>            Do you know the reason?
> 
>            Thanks a lot,
> 
>            Stefano
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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