gmx-confrms - Fit two structures and calculates the RMSD

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                    GMX-CONFRMS(1)

gmxconfrms computes the root mean square deviation (RMSD) of two structures after least-squares fitting
       the second structure on the first one.  The two structures do NOT need to have the same number of  atoms,
       only  the  two  index  groups used for the fit need to be identical.  With -name only matching atom names
       from the selected groups will be used for the fit and RMSD calculation. This can be useful when comparing
       mutants of a protein.

       The superimposed structures are written to file. In a .pdb file the two structures  will  be  written  as
       separate  models  (use  rasmol-nmrpdb).  Also  in a .pdb file, B-factors calculated from the atomic MSD
       values can be written with -bfac.

       gmx-confrms - Fit two structures and calculates the RMSD

       Options to specify input files:

       -f1[<.tpr/.gro/...>](conf1.gro)
              Structure+mass(db): tprgrog96pdb brk ent

       -f2[<.gro/.g96/...>](conf2.gro)
              Structure file: grog96pdb brk ent esp tpr-n1[<.ndx>](fit1.ndx)(Optional)
              Index file

       -n2[<.ndx>](fit2.ndx)(Optional)
              Index file

       Options to specify output files:

       -o[<.gro/.g96/...>](fit.pdb)
              Structure file: grog96pdb brk ent esp

       -no[<.ndx>](match.ndx)(Optional)
              Index file

       Other options:

       -[no]w(no)
              View output .xvg, .xpm, .eps and .pdb files

       -[no]one(no)
              Only write the fitted structure to file

       -[no]mw(yes)
              Mass-weighted fitting and RMSD

       -[no]pbc(no)
              Try to make molecules whole again

       -[no]fit(yes)
              Do least squares superposition of the target structure to the reference

       -[no]name(no)
              Only compare matching atom names

       -[no]label(no)
              Added chain labels A for first and B for second structure

       -[no]bfac(no)
              Output B-factors from atomic MSD values

gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

          gmx confrms [-f1[<.tpr/.gro/...>]] [-f2[<.gro/.g96/...>]]
                      [-n1[<.ndx>]] [-n2[<.ndx>]] [-o[<.gro/.g96/...>]]
                      [-no[<.ndx>]] [-[no]w] [-[no]one] [-[no]mw] [-[no]pbc]
                      [-[no]fit] [-[no]name] [-[no]label] [-[no]bfac]