gmx-dos - Analyze density of states and properties based on that

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                        GMX-DOS(1)

gmxdos  computes  the  Density  of  States  from a simulations.  In order for this to be meaningful the
       velocities must be saved in the trajecotry  with  sufficiently  high  frequency  such  as  to  cover  all
       vibrations.  For  flexible  systems that would be around a few fs between saving. Properties based on the
       DoS are printed on the standard output.   Note  that  the  density  of  states  is  calculated  from  the
       mass-weighted  autocorrelation,  and  by  default  only from the square of the real component rather than
       absolute value. This means the shape can differ substantially from the plain vibrational  power  spectrum
       you can calculate with gmx velacc.

       • This program needs a lot of memory: total usage equals the number of atoms  times  3  times  number  of
         frames times 4 (or 8 when run in double precision).

       gmx-dos - Analyze density of states and properties based on that

       Options to specify input files:

       -f[<.trr/.cpt/...>](traj.trr)
              Full precision trajectory: trrcpttng-s[<.tpr>](topol.tpr)
              Portable xdr run input file

       -n[<.ndx>](index.ndx)(Optional)
              Index file

       Options to specify output files:

       -vacf[<.xvg>](vacf.xvg)
              xvgr/xmgr file

       -mvacf[<.xvg>](mvacf.xvg)
              xvgr/xmgr file

       -dos[<.xvg>](dos.xvg)
              xvgr/xmgr file

       -g[<.log>](dos.log)
              Log file

       Other options:

       -b<time>(0)
              Time of first frame to read from trajectory (default unit ps)

       -e<time>(0)
              Time of last frame to read from trajectory (default unit ps)

       -dt<time>(0)
              Only use frame when t MOD dt = first time (default unit ps)

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

       -xvg<enum>(xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -[no]v(yes)
              Be loud and noisy.

       -[no]recip(no)
              Use cm^-1 on X-axis instead of 1/ps for DoS plots.

       -[no]abs(no)
              Use  the  absolute value of the Fourier transform of the VACF as the Density of States. Default is
              to use the real component only

       -[no]normdos(no)
              Normalize the DoS such that it adds up to 3N. This should usually not be necessary.

       -T<real>(298.15)
              Temperature in the simulation

       -acflen<int>(-1)
              Length of the ACF, default is half the number of frames

       -[no]normalize(yes)
              Normalize ACF

       -P<enum>(0)
              Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3

       -fitfn<enum>(none)
              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9

       -beginfit<real>(0)
              Time where to begin the exponential fit of the correlation function

       -endfit<real>(-1)
              Time where to end the exponential fit of the correlation function, -1 is until the end

gmx(1)

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

          gmx dos [-f[<.trr/.cpt/...>]] [-s[<.tpr>]] [-n[<.ndx>]]
                  [-vacf[<.xvg>]] [-mvacf[<.xvg>]] [-dos[<.xvg>]]
                  [-g[<.log>]] [-b<time>] [-e<time>] [-dt<time>] [-[no]w]
                  [-xvg<enum>] [-[no]v] [-[no]recip] [-[no]abs] [-[no]normdos]
                  [-T<real>] [-acflen<int>] [-[no]normalize] [-P<enum>]
                  [-fitfn<enum>] [-beginfit<real>] [-endfit<real>]