Provided by: gromacs-data_2018.1-1_all bug


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


          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>] [-toler <real>] [-acflen <int>] [-[no]normalize]
                  [-P <enum>] [-fitfn <enum>] [-beginfit <real>]
                  [-endfit <real>]


       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 to specify input files:

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

       -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

       -toler <real> (1e-06)
              [HIDDEN]Tolerance when computing the fluidicity using bisection algorithm

       -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


       · 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).



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       2018, GROMACS development team