.. _gmx velacc: gmx velacc ========== Synopsis -------- .. parsed-literal:: gmx velacc [:strong:`-f` :emphasis:`[<.trr/.cpt/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-o` :emphasis:`[<.xvg>]`] [:strong:`-os` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`] [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-[no]m`] [:strong:`-[no]recip`] [:strong:`-[no]mol`] [:strong:`-acflen` :emphasis:`<int>`] [:strong:`-[no]normalize`] [:strong:`-P` :emphasis:`<enum>`] [:strong:`-fitfn` :emphasis:`<enum>`] [:strong:`-beginfit` :emphasis:`<real>`] [:strong:`-endfit` :emphasis:`<real>`] Description ----------- ``gmx velacc`` computes the velocity autocorrelation function. When the ``-m`` option is used, the momentum autocorrelation function is calculated. With option ``-mol`` the velocity autocorrelation function of molecules is calculated. In this case the index group should consist of molecule numbers instead of atom numbers. By using option ``-os`` you can also extract the estimated (vibrational) power spectrum, which is the Fourier transform of the velocity autocorrelation function. Be sure that your trajectory contains frames with velocity information (i.e. ``nstvout`` was set in your original :ref:`.mdp <mdp>` file), and that the time interval between data collection points is much shorter than the time scale of the autocorrelation. Options ------- Options to specify input files: ``-f`` [<.trr/.cpt/...>] (traj.trr) Full precision trajectory: :ref:`trr` :ref:`cpt` :ref:`tng` ``-s`` [<.tpr/.gro/...>] (topol.tpr) (Optional) Structure+mass(db): :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`pdb` brk ent ``-n`` [<.ndx>] (index.ndx) (Optional) Index file Options to specify output files: ``-o`` [<.xvg>] (vac.xvg) xvgr/xmgr file ``-os`` [<.xvg>] (spectrum.xvg) (Optional) xvgr/xmgr 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 :ref:`.xvg <xvg>`, :ref:`.xpm <xpm>`, :ref:`.eps <eps>` and :ref:`.pdb <pdb>` files ``-xvg`` <enum> (xmgrace) xvg plot formatting: xmgrace, xmgr, none ``-[no]m`` (no) Calculate the momentum autocorrelation function ``-[no]recip`` (yes) Use cm^-1 on X-axis instead of 1/ps for spectra. ``-[no]mol`` (no) Calculate the velocity acf of molecules ``-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 end .. only:: man See also -------- :manpage:`gmx(1)` More information about |Gromacs| is available at <http://www.gromacs.org/>.