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
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:
Portable xdr run input file
-n[<.ndx>] (index.ndx) (Optional)
Options to specify output files:
Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
xvg plot formatting: xmgrace, xmgr, none
Be loud and noisy.
Use cm^-1 on X-axis instead of 1/ps for DoS plots.
Use the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only
Normalize the DoS such that it adds up to 3N. This should usually not be necessary.
Temperature in the simulation
[HIDDEN]Tolerance when computing the fluidicity using bisection algorithm
Length of the ACF, default is half the number of frames
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
Time where to begin the exponential fit of the correlation function
Time where to end the exponential fit of the correlation function, -1 is until the end
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).