GROMACS version:2022.3
GROMACS modification: No
Here, post your question: I am trying to simulate a protein + solvent system, but after a certain step, it starts showing the LINCS warning. My protein is coarse-grained using the MARTINI force field. I want to use the time step as 0.02 fs. However, my protein is not stabilized due to its size and poor initial structure. That’s why I have to use 0.005 fs otherwise it shows a LINCS warning.
Do you mean that your have to use a 0.005 fs timestep to avoid the LINCS warning? Or do you still get the warning?
It is quite common that you have to run (large?) parts of the equilibration with a shorter time step. If you still get a LINCS error, I would suggest having a look at your pressure coupling settings as they can sometimes cause system instabilities.