File input/output error: md_1_step3238100.cpt

User discussions
1

GROMACS version: gmx mdrun, version 2019.3
GROMACS modification: No

I simulated a system of Asphaltene structure with a solvent for 80ns simulation time, 40000000 steps. After 34 hours the job stopped and the output file reads:

File input/output error:
md_1_step3238100.cpt

I check this issue here and found this answer (File input/output error).

But, I am not satisfied yet. Any other reason for this error? And how to deal with it?

Should I run this simulation from the beginning or start from the step, where it stopped?

md.mdp (2.8 KB)

Command line: gmx mdrun -deffnm md_1

Reading file md_1.tpr, VERSION 2019.3 (single precision)

WARNING: This run will generate roughly 13269 Mb of data

starting mdrun ‘Asp_box’
40000000 steps, 80000.0 ps.

Program: gmx mdrun, version 2019.3
Source file: src/gromacs/utility/futil.cpp (line 441)

File input/output error:
md_1_step3238100.cpt

2

Hi,

An other reason can be that you are over quota or you have fill up a disk. (but normally you get a warning also from the system).
If your files are not corrupted, you can restart the simulation.
If cpt files are corrupted, you can create a new tpr file with gmx grompp. "Starting coordinates can be read from trajectory with -t . The last frame with coordinates and velocities will be read, unless the -time option is used. An energy file can be supplied with -e to read Nose-Hoover and/or Parrinello-Rahman coupling variables.
See http://manual.gromacs.org/current/onlinehelp/gmx-grompp.html

Best regards
Alessandra

3

Thank you, Alessandra. I will try your comments.

Pulok