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GMX-DOS(1) GROMACS GMX-DOS(1) NAME gmx-dos - Analyze density of states and properties based on that SYNOPSIS 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>] [-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 traje- cotry 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 auto- correlation, and by default only from the square of the real component rather than absolute value. This means the shape can differ substan- tially from the plain vibrational power spectrum you can calculate with gmx velacc. OPTIONS 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 usu- ally 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, exp5, exp7, exp9 -beginfit <real> (0) Time where to begin the exponential fit of the correlation func- tion -endfit <real> (-1) Time where to end the exponential fit of the correlation func- tion, -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 gmx(1) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-DOS(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | KNOWN ISSUES | SEE ALSO | COPYRIGHT
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