Main Table of Contents

Wed 13 Nov 2013


g_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 standard output.


-f traj.trr Input Full precision trajectory: trr trj cpt
-s topol.tpr Input Run input file: tpr tpb tpa
-n index.ndx Input, Opt. Index file
-vacf vacf.xvg Output xvgr/xmgr file
-mvacf mvacf.xvg Output xvgr/xmgr file
-dos dos.xvg Output xvgr/xmgr file
-g dos.log Output Log file

Other options

-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]v bool yes Be loud and noisy.
-[no]recip bool no Use cm^-1 on X-axis instead of 1/ps for DoS plots.
-[no]abs bool 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 bool no Normalize the DoS such that it adds up to 3N. This is a hack that should 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 bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of correlation functions
-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

Known problems