Hello everyone, i have problem when i do gromacs simulation for protein-ligand complex

Tool Standard Error
/data/jwd05e/main/064/671/64671535/tool_script.sh: line 26: 3429218 Segmentation fault (core dumped) gmx mdrun -nt “${GALAXY_SLOTS:-4}” -deffnm outp &>> verbose.txt

  • { “code_desc”: “”, “desc”: “Fatal error: Exit code 139 ()”, “error_level”: 3, “exit_code”: 139, “type”: “exit_code” }

Welcome, @Howida_Nail

An error like this:

means that the tool completely died out and nothing could be rescued.

You could try a rerun. The public servers process many thousands of jobs each day. Some can fail by chance.

Other reasons can be problematic inputs or parameters – but try the rerun first before troubleshooting the other details.

Tutorial with example data and a workflow template: Running molecular dynamics simulations using GROMACS

Thank you, Jennaj, for your response. I’ve attempted to rerun the simulation multiple times, but I’m consistently encountering the same error. The energy minimization step in GROMACS produces satisfactory results, but the error arises when I proceed to the subsequent simulation step. I’m trying to identify the reasons behind this issue.

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