Synopsis
gmx dos [-f [<.trr/.cpt/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
[-vacf [<.xvg>]] [-mvacf [<.xvg>]] [-dos [<.xvg>]] [-g [<.log>]]
[-nice ] [-b ] [-e ] [-dt ] [-[no]w]
[-xvg ] [-[no]v] [-[no]recip] [-[no]abs] [-[no]normdos]
[-T ] [-acflen ] [-[no]normalize] [-P ]
[-fitfn ] [-beginfit ] [-endfit ]
Description
gmx 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.
Options
Options to specify input and output files:
-f trr /.cpt /...>] (traj.trr ) (Input)
Full precision trajectory: trr cpt trj tng
-s tpr /.tpb /...>] (topol.tpr ) (Input)
Run input file: tpr tpb tpa
-n ndx >] (index.ndx ) (Input, Optional)
Index file
-vacf xvg >] (vacf.xvg ) (Output)
xvgr/xmgr file
-mvacf xvg >] (mvacf.xvg ) (Output)
xvgr/xmgr file
-dos xvg >] (dos.xvg ) (Output)
xvgr/xmgr file
-g log >] (dos.log ) (Output)
Log file
Other options:
-nice
Set the nicelevel
-b
First frame (ps) to read from trajectory
-e
Last frame (ps) to read from trajectory
-dt
Only use frame when t MOD dt = first time (ps)
-[no]w
View output .xvg , .xpm , .eps and .pdb files
-xvg
xvg plot formatting: xmgrace, xmgr, none
-[no]v
Be loud and noisy.
-[no]recip
Use cm^-1 on X-axis instead of 1/ps for DoS plots.
-[no]abs
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
Normalize the DoS such that it adds up to 3N. This is a hack that should not be necessary.
-T
Temperature in the simulation
-acflen
Length of the ACF, default is half the number of frames
-[no]normalize
Normalize ACF
-P
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
-fitfn
Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9, erffit
-beginfit
Time where to begin the exponential fit of the correlation function
-endfit
Time where to end the exponential fit of the correlation function, -1 is until the end
Known Issues
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).
