[gmx-users] problem with system neutralization

[Justin A. Lemkul]

Stefano Meliga wrote:
> 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
> 

The logfile should report what the net charge is; this is normal.  What is of 
importance is whether or not the output structure and topology have been 
modified to include the desired ions.  If grompp later complains that there is 
still a net charge, then you have a problem.

-Justin

> 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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-- 
========================================

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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