[gmx-users] re K+ ion

[Yang Ye]

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
/