Regarding to use Shake to fix bond for bulk water in DFT

Pankaj Mishra pkmis... at
Fri Dec 12 16:22:33 UTC 2014

Dear all,

I am trying to use shake for bulk simulation via DFT.  Suppose i am trying 
to fix bond for water molecules, then how can i fix the  distance between 
oxygen and hydrogen of water? I mean do i need to define bond for each 
bonded atom pair separately for distance in  COLVAR ? Is there some way to 
define molecule? For DFT calculation, i am just using atom ID (O or H) and 
its positions in random order. I am trying with  CONSTRAINT 
but there are confusions, like how to define molecule as we don,t need to 
give bond and angle information in CP2K for DFT calculation. Here i am 
attaching my input file. I hope that will help you to understand my 
I hope for some suggestions. 

Thank you so much

Pankaj Mishra
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