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

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

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

18       gmx  dos  computes  the Density of States from a simulations.  In order
19       for this to be meaningful the velocities must be saved  in  the  traje‐
20       cotry with sufficiently high frequency such as to cover all vibrations.
21       For flexible systems that would be around  a  few  fs  between  saving.
22       Properties  based  on the DoS are printed on the standard output.  Note
23       that the density of states is calculated from the  mass-weighted  auto‐
24       correlation,  and by default only from the square of the real component
25       rather than absolute value. This means the shape  can  differ  substan‐
26       tially from the plain vibrational power spectrum you can calculate with
27       gmx velacc.
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OPTIONS

30       Options to specify input files:
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32       -f [<.trr/.cpt/…>] (traj.trr)
33              Full precision trajectory: trr cpt tng
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35       -s [<.tpr>] (topol.tpr)
36              Portable xdr run input file
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38       -n [<.ndx>] (index.ndx) (Optional)
39              Index file
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41       Options to specify output files:
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43       -vacf [<.xvg>] (vacf.xvg)
44              xvgr/xmgr file
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46       -mvacf [<.xvg>] (mvacf.xvg)
47              xvgr/xmgr file
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49       -dos [<.xvg>] (dos.xvg)
50              xvgr/xmgr file
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52       -g [<.log>] (dos.log)
53              Log file
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55       Other options:
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57       -b <time> (0)
58              Time of first frame to read from trajectory (default unit ps)
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60       -e <time> (0)
61              Time of last frame to read from trajectory (default unit ps)
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63       -dt <time> (0)
64              Only use frame when t MOD dt = first time (default unit ps)
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66       -[no]w (no)
67              View output .xvg, .xpm, .eps and .pdb files
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69       -xvg <enum> (xmgrace)
70              xvg plot formatting: xmgrace, xmgr, none
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72       -[no]v (yes)
73              Be loud and noisy.
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75       -[no]recip (no)
76              Use cm^-1 on X-axis instead of 1/ps for DoS plots.
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78       -[no]abs (no)
79              Use the absolute value of the Fourier transform of the  VACF  as
80              the Density of States. Default is to use the real component only
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82       -[no]normdos (no)
83              Normalize  the  DoS such that it adds up to 3N. This should usu‐
84              ally not be necessary.
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86       -T <real> (298.15)
87              Temperature in the simulation
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89       -toler <real> (1e-06)
90              [HIDDEN]Tolerance when computing the fluidicity using  bisection
91              algorithm
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93       -acflen <int> (-1)
94              Length of the ACF, default is half the number of frames
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96       -[no]normalize (yes)
97              Normalize ACF
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99       -P <enum> (0)
100              Order  of  Legendre polynomial for ACF (0 indicates none): 0, 1,
101              2, 3
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103       -fitfn <enum> (none)
104              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
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106       -beginfit <real> (0)
107              Time where to begin the exponential fit of the correlation func‐
108              tion
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110       -endfit <real> (-1)
111              Time  where  to end the exponential fit of the correlation func‐
112              tion, -1 is until the end
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KNOWN ISSUES

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

120       gmx(1)
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122       More    information    about    GROMACS    is    available    at     <‐
123       http://www.gromacs.org/>.
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126       2020, GROMACS development team
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1312019.6                           Feb 28, 2020                       GMX-DOS(1)
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