I’m using the eqA.mdp file from the tutorial here:
Despite running several equilibration steps with and without restraints on my ligand I get the error:
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001067, max 0.057983 (between atoms 9731 and 9732)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
I can see the dummy atoms swinging around like crazy when I visualize the equilibration trajectory. I don’t know why the equilibration doesn’t crash but the run started from the provided mdp file does.
Apparently an mdp setting I need to adjust?
Or is it an issue with my ligand structure? I can’t see why this would be the case since this is a structure I’ve used in many simulations (without the dummy atoms).