GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  GMX-DOS (1)

NAME

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

CONTENTS

Synopsis
Description
Options
Known Issues
See Also

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. 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 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, erffit

-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 ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.

Search for    or go to Top of page |  Section 1 |  Main Index


VERSION 5.0.6 GMX-DOS (1)

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.