[gmx-users] ion jump out of protein

[Justin A. Lemkul]

Homa Azizian wrote:
> Hi 
> I mean after MD the ion was not in the active site, the location of ion is 
> out of the protein.
> 

Then your model physics is wrong and you will have to re-think/re-derive 
appropriate parameters.

-Justin

>> My ion jump out of the protein after MD.My ion (MN) has not any covalant 
>> bond by its neibour, just has electrostatic intraction. 
>> is there any line that I have to add to the itp file or top file in order 
>> to 
>> prevent this problem. 
>>
> 
> --
> Tehran University of Medical Sciences
> www.tums.ac.ir
> 
> 

-- 
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Justin A. Lemkul
Graduate Research Assistant
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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