GROMACS version:
GROMACS modification: Yes/No
Here post your question
Note:
The bond in molecule-type CHYO between atoms 1 R0 and 2 R1 has an
estimated oscillational period of 2.1e-01 ps, which is less than 10 times
the time step of 3.0e-02 ps.
Maybe you forgot to change the constraints mdp option
In constraints I used h-bonds
when I neglect the notes I started the production run
It was running fine until 0.6us after that it started blown up throwing step files and linics warning
Fatal error:
one or more atoms moved too far between domain decomposition steps
this usually means that your system is not well equilibrated
Kindly help me with this
Could you provide details on what system you’re simulating, what commands you used to set up the simulation, and any additional notes/warnings/errors you encountered during each step? The more information, the easier it is to help