table of contents
g_dos(1) | GROMACS suite, VERSION 4.5.5 | g_dos(1) |
NAME¶
g_dos - compute density of states from a simulation trajectory VERSION 4.5.5SYNOPSIS¶
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 realDESCRIPTION¶
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.FILES¶
-f traj.trr InputFull precision trajectory: trr trj cpt
Run input file: tpr tpb tpa
Index file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
Log file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Be loud and noisy.
Use cm-1 on X-axis instead of 1/ps for DoS plots.
Use the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only
Normalize the DoS such that it adds up to 3N. This is a hack that should not be necessary.
Temperature in the simulation
Length of the ACF, default is half the number of frames
Normalize ACF
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit
Skip N points in the output file of correlation functions
Time where to begin the exponential fit of the correlation function
Time where to end the exponential fit of the correlation function, -1 is until the end
KNOWN PROBLEMS¶
- 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¶
gromacs(7)Wed 21 Sep 2011 |