[gmx-users] Coordinates change after minimization

Justin A. Lemkul jalemkul at vt.edu
Sat Jun 20 13:32:24 CEST 2009

Ms. Aswathy S wrote:
> Hi,
> After minimizing the protein -ligand complex, the co-ordinates have changed
> drastically.My idea about minimization was the coordinates will have minute
> changes only. In this case my protein is completely transferring to a new
> co-ordinates.Is that reasonable.??

The amount of change will depend on the quality of the initial model.  If large 
changes need to be made, they can be.  If the entire protein is moving, then 
perhaps the box has not been prepared correctly, and the translation is caused 
by a periodic jump.  Have a look at the output (not just the coordinates) and 
see if you can deduce what's going on.


> Thanks, Aswathy Dept. Biotechnology Ext. 3108 
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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


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