[gmx-users] problem with system neutralization

[Pawan Kumar]

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> 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>> 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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