GROMACS version:2025.2
GROMACS modification: No
I merged the RMSD.xvg and Rgrate.xvg files to generate the rmsd_rg_combined.xvg file, used gmx sham to generate the gibbs.xpm file, and the command produced the following prompt:
root@xxxxx:~/ligand# gmx sham -f rmsd_rg_combined.xvg -ls gibbs.xpm -nlevels 100 -tsham 300
:-) GROMACS - gmx sham, 2025.2 (-:Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /root/ligand
Command line:
gmx sham -f rmsd_rg_combined.xvg -ls gibbs.xpm -nlevels 100 -tsham 300
Read 1 sets of 10001 points, dt = 6.45775e-05
There are 32 bins in the 1-dimensional histogram. Beta-Emin = 0
Ptot = 10001
Back Off! I just backed up ener.xvg to ./#ener.xvg.5#
Back Off! I just backed up bindex.ndx to ./#bindex.ndx.5#
Back Off! I just backed up shamlog.log to ./#shamlog.log.5#
GROMACS reminds you: “C has the power of assembly language and the convenience of… assembly language.” (Dennis Ritchie)
The command will not report errors. It will only generate shamlog.log, bindex.ndx and ener.xvg files, but will not generate gibbs.xpm files.
The merge command of RMSD.xvg and Rgrate.xvg files is:
paste <(awk ‘!/[@#]/ {print $2}’ RMSD.xvg) <(awk ‘!/[@#]/ {print $2}’ Rgrate.xvg) > rmsd_rg_combined.xvg