[gmx-users] problem with system neutralization

[Stefano Meliga]

Hi again,

Apologies for my last imprecise email.

Using the command

$grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb

genion.log still reports:

System total charge: -4.000

Stefano

2009/5/22, Pawan Kumar <pawan.chinari at gmail.com>:
> 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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