[gmx-users] energy minimization breaks freeze group apart

Patricia Francis-Lyon patflyon at hotmail.com
Sun Jan 27 06:40:20 CET 2008

I want to do energy minimization on a loop that had been missing and was filled in by  modloop, while freezing the rest of the protein. 
Before the minimization I have an SO4 ion and 135 water molecules from the crystallography around the protein. After the minimization the protein has been translated in the y direction away from the water and SO4. 
My freeze group is :
0 & ! 15 which is System and not loop. 
I’m confused about why part of the freeze group (the protein) is translated away from the other part (So4 + crystal water). This happens with both steep and l-bfgs.
Thanks for your help!
Patricia Francis-Lyon
Shed those extra pounds with MSN and The Biggest Loser!
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