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 0

Ignoring 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