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GMX-DOS(1)			     GROMACS			      GMX-DOS(1)

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

SYNOPSIS
	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>]

DESCRIPTION
     gmx  dos  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.

OPTIONS
     Options to specify input files:

     -f [<.trr/.cpt/...>] (traj.trr)
	    Full precision trajectory: trr cpt tng h5md

     -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

KNOWN ISSUES
     * 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).

SEE ALSO
     gmx(1)

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

COPYRIGHT
     2026, GROMACS development team

2026.3				  Jun 25, 2026			      GMX-DOS(1)
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