GROMACS version:5.1.2
GROMACS modification: Yes/No
I am trying protein ligand complex simulation using gr
em.mdp (1.1 KB)
omacs while performing energy minimization step using the command "gmx mdrun -deffnm em "
fatal error ocurred:
step 22 : water molecules starting at atom 7488 can not be settled. Check for bad contacts and/or reduce the time steps if appropriate .
i want to know how to resolve this error and if i reduce timestep does it effect my final results analysis or not and how to reduce time steps in .mdp file
thank you in advance
enclosing my parameters file
When it crashes already during energy minimization you almost certainly have atoms that are overlapping or colliding, alternatively very poor molecular geometries. Overlapping could be caused by system dimensions not being correct.
Open your input coordinates in, e.g., VMD and see if you can find any overlapping atoms. Start looking in the region around atom 7488. Also check that the periodic box encloses the whole system, with a small margin. You can view the periodic box with pbc box in VMD.