gmx-dos(1) GROMACS Manual gmx-dos(1)NAMEgmx-dos - Analyze density of states and properties based on that
SYNOPSIS
gmx dos [-f [<.trr/.cpt/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
[-vacf [<.xvg>]] [-mvacf [<.xvg>]] [-dos [<.xvg>]]
[-g [<.log>]] [-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>]
[-beginfit <real>] [-endfit <real>]
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. Proper‐
ties based on the DoS are printed on the standard output.Note that the
density of states is calculated from the mass-weighted autocorrelation,
and by default only from the square of the real component rather than
absolute value. This means the shape can differ substantially from the
plain vibrational power spectrum you can calculate with gmx velacc.
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 <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 (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]v (yes)
Be loud and noisy.
-[no]recip (no)
Use cm-1 on X-axis instead of 1/ps for DoS plots.
-[no]abs (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 (no)
Normalize the DoS such that it adds up to 3N. This should usually
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 (yes)
Normalize ACF
-P <enum> (0)
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
-fitfn <enum> (none)
Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9, erf‐
fit
-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 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).
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-dos(1)
