Continuing the discussion from "Assertion failed" error when running the BAR command:
I have the same issue. I post the md*.file I created using the Free Energy Calculations
The output md* files are posted on this site.
Just output files
I have newly installed Ubuntu & 2023.3 GROMACS.
It still gives me the same error. Thank you very much.
That sounds strange. I tested your files and gmx bar -f md*.xvg ran fine, admittedly using the current main development branch of Gromacs, but I don’t see why 2023.3 would be different in this case. What’s the exact command you used to run gmx bar? Does a normal simulation run with that Gromacs installation? Does other analysis tools work?
I used exactly what the tutorial suggested. gmx bar -f md*.xvg -o -oi
On the previous version (I reinstall Linux so I lost the previous working version)
I created xvg files and analysis worked okay at that time. I had those xvg files in the backup disk so I tried to analyze the old data using new version of GROMACS. However, new version gave me the same error (same as Tutorial). I will try to uninstall and reinstall the GROMACS again. I will post the question again if I see the same issue. Thank you very much for your help.
Executable: /usr/local/bin/gmx
Data prefix: /usr/local
Working dir: /home/Me/Desktop/0repeat/1st/Prod
Command line:
gmx bar -b 30 -f dhdl0.xvg dhdl10.xvg dhdl11.xvg dhdl12.xvg dhdl13.xvg dhdl14.xvg dhdl15.xvg dhdl16.xvg dhdl17.xvg dhdl18.xvg dhdl19.xvg dhdl1.xvg dhdl20.xvg dhdl2.xvg dhdl3.xvg dhdl4.xvg dhdl5.xvg dhdl6.xvg dhdl7.xvg dhdl8.xvg dhdl9.xvg -o -oi
dhdl0.xvg: Ignoring set ‘pV (kJ/mol)’.
Program: gmx bar, version 2023.3
Source file: src/gromacs/gmxana/gmx_bar.cpp (line 743)
Function: sample_coll_insert_sample(sample_coll_t*, samples_t*, sample_range_t*)::<lambda()>
Assertion failed:
Condition: sc->next->s
Next not properly initialized!
If you run into the same problem after the reinstallation of GROMACS it would be interesting to see if the test suite passes. I.e., if it works when you run make check where you built your GROMACS installation.
During the previous installation, I missed the error message “Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version “4.0.0”)”
After installing “python3-sphinx”, and installing from home directly, it worked out. Thank you very much for the help. Now, it does BAR analysis.