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.