File input/output error

User discussions
1

GROMACS version: 5.1.4
I simulated a system of RBMX protein in 0.1mol/L NaCl on the cluster of my department, with 2000ns simulation time, 1000000000 steps. After 5 days the job stopped and the output file reads:
File input/output error :
md_0_1_step46636660.cpt

What is the reason of this error? And how to deal with it?

Thanks for your help!

2

This sounds like an issue with your cluster, possibly the cluster filesystem has an issue or there is a connection issue on the cluster. If something like this happens, it’s also useful to run gmx check -f [yourtrajectory] to make sure that your trajectory is still okay.

3

Thanks a lot! Indeed there is an error in my trajectory.