Hi all, I am trying to build an elastic network model using only C-alpha atoms . Potential energy function contains only bond stretching energy term rest like angle,dihedral and non bonded are not included. I use bond function type(f.tp = 6) ,i.e. is harmonic bond potential . The problem is that atoms connected by harmonic potential are rotating . I do not want to use any constraints. How can I fix this ?
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