Troubleshooting a GROMACS termination following “Generating 1-4 interactions: fudge = 1”
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Hi everyone,
Nice to be here. I am new to GROMACS and I am trying to simulate an RNA polymerase extension. GROMACS wizard terminates with only the following log given:
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Executable: C:\Users\username\AppData\Local\OneAngstrom\SAMSON-Data\6.0.1\Scratch\Elements\02407D21-0490-30BA-D20F-2E88DB100FC5\Resource\gromacs\gmx.exe
Data prefix: C:\Program Files (x86)\Gromacs
Working dir: C:\Users\username\AppData\Local\OneAngstrom\SAMSON-Data\6.0.1\Scratch\GROMACS\48B611E7-078C-4404-28D5-C6BCA715CAE4
Command line:
gmx grompp -f md.mdp -c step4_input.gro -p step4_input.top -n index.ndx -po step4_input_md_mdout.mdp -o step4_input_md.tpr -maxwarn 0Ignoring obsolete mdp entry ‘rlistlong’
Ignoring obsolete mdp entry ‘nstcalclr’
Ignoring obsolete mdp entry ‘ns-type’
Generating 1-4 interactions: fudge = 1
–
And no more than that. As there is no warning/description, it is difficult to trace the error and fix it.
GROMACS wizard (directly starting from step5 simulation) on SAMSON was run in Windows. The input files (.gro, .top and the associated .itp, .mdp (step 6)) were generated by the multicomponent assembler on CHARMM-GUI. The .gro, .top, and .mdp files were renamed to “step4_input.xxx”. SAMSON itself was able to present the solvated polymerase on the graphical interface.
Would anyone educate me on where to start with? I am ready to inspect files and provide information per their suggestion. Big thanks to everyone.
LW
-
Hi everyone,
Nice to be here. I am new to GROMACS and I am trying to simulate an RNA polymerase extension. GROMACS wizard terminates with only the following log given:
–
Executable: C:\Users\username\AppData\Local\OneAngstrom\SAMSON-Data\6.0.1\Scratch\Elements\02407D21-0490-30BA-D20F-2E88DB100FC5\Resource\gromacs\gmx.exe
Data prefix: C:\Program Files (x86)\Gromacs
Working dir: C:\Users\username\AppData\Local\OneAngstrom\SAMSON-Data\6.0.1\Scratch\GROMACS\48B611E7-078C-4404-28D5-C6BCA715CAE4
Command line:
gmx grompp -f md.mdp -c step4_input.gro -p step4_input.top -n index.ndx -po step4_input_md_mdout.mdp -o step4_input_md.tpr -maxwarn 0Ignoring obsolete mdp entry ‘rlistlong’
Ignoring obsolete mdp entry ‘nstcalclr’
Ignoring obsolete mdp entry ‘ns-type’
Generating 1-4 interactions: fudge = 1
–
And no more than that. As there is no warning/description, it is difficult to trace the error and fix it.
GROMACS wizard (directly starting from step5 simulation) on SAMSON was run in Windows. The input files (.gro, .top and the associated .itp, .mdp (step 6)) were generated by the multicomponent assembler on CHARMM-GUI. The .gro, .top, and .mdp files were renamed to “step4_input.xxx”. SAMSON itself was able to present the solvated polymerase on the graphical interface.
Would anyone educate me on where to start with? I am ready to inspect files and provide information per their suggestion. Big thanks to everyone.
LW
Hi,
Did you perform other steps (preparation, minimization, equilibration) in GROMACS Wizard before running the production MD (see GROMACS Wizard tutorials)? If not, you might want to try to run them starting from the preparation step.
Could you share the input (all the input files for the step) and resulting files (the corresponding folder into which GROMACS Wizard saved the resulting files, named with a time stamp, e.g. "2024-10-23_09h55m26s-simulate-error") with us so we can try to reproduce the issue and see is the problem?
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