[gmx-users] Simulation crashed, fatal error: Bond length not finite and warning: Pressure scaling more than 1%.

[zeineb SI CHAIB]

Dear all,


Thank you for your suggestions and help.


@Quyen, I checked the energies, box fluctuations and pressure deviations and everything seem correct: Energies (potential, kinetic and total) were stable during the simulation and the average of the pressure was 1.04 bar.


@ Peter, I equilibrated my system for 50ns (NPT equilibration followed by NVT equilibration, both during 50ns each one). Also, the system crashed after 2.5 μs of simulation.


@ Kevin,  I run the simulation with the option -rdd 1.5 but the system crashed in the same step with the same error: Fatal error: bond length not finite. I also noticed that before crashing, I had too many LINCS warning!


I still don't see where could be the problem, especially that everything was good for 2.5μs of simulation...



Best,


Zeineb