[lammps-users] fix shake

Dear lammps user,

I am running a simulation on a protein structure. In this simulation, shake algorithm was used to constrain bonds. This is the way that I defined fix shake:
fix 1 all shake 0.0001 500 0 m 1.008

Here I constrained bond lengths including hydrogen.
The problem I have is that the final structure after the simulation is not conserved but the result looks promising when I don’t include shake algorithm in my simulation.
Can you please tell me if any consideration needs to be taken into the account for shake algorithm in my code?
Additionally, I will be thankful to know if it is possible to constrain all bond lengths in a simulation in Lammps.

Your description is far too vague to provide any specific suggestions. Also, your observations and conclusions are inconsistent with typical simulations.

The limitations of fix shake are explained in its documentation.