1GMX-DOS(1) GROMACS GMX-DOS(1)
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6 gmx-dos - Analyze density of states and properties based on that
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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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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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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‐
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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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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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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 2019, GROMACS development team
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1312019.4 Oct 02, 2019 GMX-DOS(1)