This is the command gmx-rmsf 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-rmsf - Calculate atomic fluctuations
SYNOPSIS
gmx rmsf [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-q [<.pdb>]] [-oq [<.pdb>]] [-ox [<.pdb>]] [-o [<.xvg>]]
[-od [<.xvg>]] [-oc [<.xvg>]] [-dir [<.log>]] [-b <time>]
[-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]res]
[-[no]aniso] [-[no]fit]
DESCRIPTION
gmx rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of
atomic positions in the trajectory (supplied with -f) after (optionally) fitting to a
reference frame (supplied with -s).
With option -oq the RMSF values are converted to B-factor values, which are written to a
.pdb file with the coordinates, of the structure file, or of a .pdb file when -q is
specified. Option -ox writes the B-factors to a file with the average coordinates.
With the option -od the root mean square deviation with respect to the reference structure
is calculated.
With the option -aniso, gmx rmsf will compute anisotropic temperature factors and then it
will also output average coordinates and a .pdb file with ANISOU records (corresonding to
the -oq or -ox option). Please note that the U values are orientation-dependent, so before
comparison with experimental data you should verify that you fit to the experimental
coordinates.
When a .pdb input file is passed to the program and the -aniso flag is set a correlation
plot of the Uij will be created, if any anisotropic temperature factors are present in the
.pdb file.
With option -dir the average MSF (3x3) matrix is diagonalized. This shows the directions
in which the atoms fluctuate the most and the least.
OPTIONS
Options to specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Optional)
Index file
-q [<.pdb>] (eiwit.pdb) (Optional)
Protein data bank file
Options to specify output files:
-oq [<.pdb>] (bfac.pdb) (Optional)
Protein data bank file
-ox [<.pdb>] (xaver.pdb) (Optional)
Protein data bank file
-o [<.xvg>] (rmsf.xvg)
xvgr/xmgr file
-od [<.xvg>] (rmsdev.xvg) (Optional)
xvgr/xmgr file
-oc [<.xvg>] (correl.xvg) (Optional)
xvgr/xmgr file
-dir [<.log>] (rmsf.log) (Optional)
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]res (no)
Calculate averages for each residue
-[no]aniso (no)
Compute anisotropic termperature factors
-[no]fit (yes)
Do a least squares superposition before computing RMSF. Without this you must make
sure that the reference structure and the trajectory match.
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