[CP2K-user] [CP2K:21252] Defining bond connectivity in CP2K for classical MD simulation

Planck rajg.chnk at gmail.com
Wed Mar 5 17:24:11 UTC 2025


Hi, 
                      I'm using CP2K to simulate N2 molecule. For the 
non-bonded potential I use an analytical potential using the GENPOT 
feature. I have 4 N2 molecules and I defined the coordinates with a PDB 
file and the connectivity with a PSF file, which is generated using the 
autoPSF module of VMD. When I start the simulation, the bonded Nitrogen 
molecule are not staying bonded: they dissociate and  move on their own. I 
have defined a Harmonic type potential for the bond and provided the K and 
the bond-length. 
Why is this happening despite me defining the bonds through PSF file?
Can anyone help me find the issue? Is there anything wrong with the syntax?


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