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gmx-dos(1)                      GROMACS Manual                      gmx-dos(1)

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

SYNOPSIS
       gmx dos [-f [<.trr/.cpt/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
               [-vacf [<.xvg>]] [-mvacf [<.xvg>]] [-dos [<.xvg>]]
               [-g [<.log>]] [-nice <int>] [-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 and output files:

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

       -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
           Run input file: tpr tpb tpa

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

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

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

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

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

       Other options:

       -nice <int> (19)
           Set the nicelevel

       -b <time> (0)
           First frame (ps) to read from trajectory

       -e <time> (0)
           Last frame (ps) to read from trajectory

       -dt <time> (0)
           Only use frame when t MOD dt = first time (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, vac, exp5, exp7, exp9,
       erffit

       -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
       gromacs(7)

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

VERSION 5.0.6                                                       gmx-dos(1)