Provided by: gromacs-data_4.6.5-1build1_all
g_dos - compute density of states from a simulation trajectory VERSION 4.5.5
g_dos -f traj.trr -s topol.tpr -n index.ndx -vacf vacf.xvg -mvacf mvacf.xvg -dos dos.xvg -g dos.log -[no]h -[no]version -nice int -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 -ncskip int -beginfit real -endfit real
g_dos computes the Density of States from a simulation. In order for this to be meaningful the velocities must be saved in the trajectory 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
-[no]hno Print help info and quit -[no]versionno 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]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]vyes Be loud and noisy. -[no]recipno Use cm-1 on X-axis instead of 1/ps for DoS plots. -[no]absno 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]normdosno 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]normalizeyes 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 N 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
- 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).
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Wed 21 Sep 2011 g_dos(1)