I wonder if this problem still condtinues in lammps sinced I couldn’t found further conversation in this regards.
I am doing similar simulation (fix_shake angle with asymmetric bond and the in output file angle fixes to a different angle than setting). I wonder if there is a solution for this problem.
Here is the part of my commands in lammps for stetting the shake fixes:
bond_coeff 1 1000.00 1.0
bond_coeff 2 1000.00 1.510
angle_coeff 1 100.0 109.47
fix 1 all shake 0.0001 20 0 b 1 2 a 1
the bonds for angle #1 are bond #1 and bond #2 but the result angle is 104 degree.
Thank you very much for reviewing this problem.