[gmx-users] ion jump out of protein

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 14 13:33:01 CET 2009

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.


>> 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


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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