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This is the command gmx-dos that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gmx-dos - Analyze density of states and properties based on that

SYNOPSIS


gmx dos [-f [<.trr/.cpt/...>]] [-s [<.tpr>]] [-n [<.ndx>]]
[-vacf [<.xvg>]] [-mvacf [<.xvg>]] [-dos [<.xvg>]]
[-g [<.log>]] [-b <time>] [-e <time>] [-dt <time>] [-[no]w]
[-xvg <enum>] [-[no]v] [-[no]recip] [-[no]abs] [-[no]normdos]
[-T <real>] [-toler <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. Properties 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 files:

-f [<.trr/.cpt/...>] (traj.trr)
Full precision trajectory: trr cpt tng

-s [<.tpr>] (topol.tpr)
Portable xdr run input file

-n [<.ndx>] (index.ndx) (Optional)
Index file

Options to specify output files:

-vacf [<.xvg>] (vacf.xvg)
xvgr/xmgr file

-mvacf [<.xvg>] (mvacf.xvg)
xvgr/xmgr file

-dos [<.xvg>] (dos.xvg)
xvgr/xmgr file

-g [<.log>] (dos.log)
Log file

Other options:

-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>
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

-toler <real> (1e-06)
[HIDDEN]Tolerance when computing the fluidicity using bisection algorithm

-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, exp5, exp7, exp9

-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).

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