[gmx-users] re K+ ion

[Yang Ye]

taveechai taveecharoenkool wrote:
> Hi Yang,
>  I don't understand what you mean, please give me an
> example.
> i see 
>  excl:
>             multinr[division over processors]: 52414 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0
>             nr=52414
>             nra=211794
>             excl[0][0..5]={0, 1, 2, 3, 4, 5}
>             excl[1][6..13]={0, 1, 2, 3, 4, 5, 6, 18}
>             excl[2][14..19]={0, 1, 2, 3, 4, 5}
>             excl[3][20..30]={0, 1, 2, 3, 4, 5, 6, 7,
> 18, 19, 20}
>             excl[4][31..38]={0, 1, 2, 3, 4, 5, 6, 18}
> what does this mean?
> Please help,
>   
excl[0][0...5] means for atom #0 (find this in your gro file) has 6 
exclusion respectively to atom #0, #1, #2,...,#5.
In your problem, you may locate the atom # for K and find its' exclusion 
list. Exclusion means there is no NB interaction between the pair.
You can also check the charge for K in the dump file.
> --- Yang Ye <leafyoung81-group at yahoo.com> wrote:
>
>   
>> use gmxdump -s to check whether there is exclusion
>> between them (look 
>> for "excl")
>>
>> taveechai taveecharoenkool wrote:
>>     
>>> Dear Jochen,
>>> thanks very much for your reply. Anyway, i already
>>>       
>> did
>>     
>>> what you suggest. I can run without the problem. I
>>> want to analyze the system after 1ns or 2ns, when
>>>       
>> i
>>     
>>> use g_saltbr which tell the oppositely two-charged
>>> groups. it doesn't have interaction of K+ and
>>>       
>> negative
>>     
>>> charge. I quite don't understand.. where my K+
>>>       
>> charge.
>>     
>>> --- Jochen Hub <jhub at gwdg.de> wrote:
>>>
>>>   
>>>       
>>>> taveechai taveecharoenkool wrote:
>>>>
>>>>     
>>>>         
>>>>> Dear all,
>>>>> I want to study the effect of K ion on a
>>>>>           
>> protein.
>>     
>>>>>       
>>>>>           
>>>> I
>>>>     
>>>>         
>>>>> add this line in ions.itp 
>>>>> [ moleculetype ]
>>>>> ; molname	nrexcl
>>>>> K+		1
>>>>> [ atoms ]
>>>>> ; id	at type res nr	residu name	at name  cg nr 
>>>>>       
>>>>>           
>>>> charge
>>>>     
>>>>         
>>>>>  mass
>>>>> 1	K+	1	K+		K	1	1	 39.0983  
>>>>> it seems ok, i can run (mdrun) without error.
>>>>>           
>> The
>>     
>>>>> thing in my mind is that is it enough (to edit
>>>>>           
>> only
>>     
>>>>> one file) cos it seems like K+ doesn't contain
>>>>> positive charge when i used g_saltbr? i use
>>>>>       
>>>>>           
>>>> Gromos96
>>>>     
>>>>         
>>>>> forcefield.
>>>>> Thanks in advance
>>>>>
>>>>>       
>>>>>           
>>>> You should add a
>>>> K+      1
>>>>
>>>> into the [ molecules ] section of your topol.top.
>>>>
>>>> And , of course, you need to place it into your
>>>> starting structure (pdb 
>>>> or gro).
>>>>
>>>> Jochen
>>>>
>>>> -- 
>>>> ************************************************
>>>> Jochen Hub
>>>> Max Planck Institute for Biophysical Chemistry
>>>> Computational biomolecular dynamics group
>>>> Am Fassberg 11
>>>> D-37077 Goettingen, Germany
>>>> Email: jhub[at]gwdg.de
>>>> ************************************************
>>>>
>>>>
>>>>
>>>>     
>>>>         
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>>>       
>> -- 
>> /Regards,/
>> Yang Ye
>> /Computational Biology Lab
>> School of Biological Sciences
>> Nanyang Technological University
>> Singapore
>> Tel: 6316-2884
>> /
>>
>>     
>
>
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>   

-- 
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/