.....help not held ..

Dear Daniel,

this error is a typical indicator for a badly equilibrated system. Maybe atoms move or bonds rotate too fast. Have a look at the specific warnings and check your system.

If everything in your system is defined correctly, additional energy minimization or equilibration with a shorter time step might help.

Best regards,

Martin

Thank you Martin, now I changed some parameters and now I am getting this error

Segmentation fault

A segmentation fault has many possible causes. Before your changes you got LINCS warnings, so I still think the system is not properly equilibrated.

Without further information about your system, I can only recommend to thoroughly check inputs and outputs of your set up, energy minimization, and equilibration.

Segmentation fault might come because of very high force value during minimisation. Try using double precision Gromacs and/or increasing the tolerance limit of energy and decreasing the step size in your mdp file.

Thank you all

You could try to do a first minimization using soft-core potentials, if the problem persists. They could do the trick for bad contacts.

Dear Alejandro, 

Thank you, how can I use soft-core potential, the problem still persist. please assist. 

Thank you