g_dos(1) compute density of states from a simulation trajectory


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 


 Print help info and quit

 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)

 View output  .xvg .xpm .eps and  .pdb files

-xvg enum xmgrace
 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.

-T real 298.15
 Temperature in the simulation

-acflen int -1
 Length of the ACF, default is half the number of frames

 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).