This is the command gmx-rmsdist 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-rmsdist - Calculate atom pair distances averaged with power -2, -3 or -6
SYNOPSIS
gmx rmsdist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-equiv [<.dat>]] [-o [<.xvg>]] [-rms [<.xpm>]]
[-scl [<.xpm>]] [-mean [<.xpm>]] [-nmr3 [<.xpm>]]
[-nmr6 [<.xpm>]] [-noe [<.dat>]] [-b <time>] [-e <time>]
[-dt <time>] [-[no]w] [-xvg <enum>] [-nlevels <int>]
[-max <real>] [-[no]sumh] [-[no]pbc]
DESCRIPTION
gmx rmsdist computes the root mean square deviation of atom distances, which has the
advantage that no fit is needed like in standard RMS deviation as computed by gmx rms.
The reference structure is taken from the structure file. The RMSD at time t is
calculated as the RMS of the differences in distance between atom-pairs in the reference
structure and the structure at time t.
gmx rmsdist can also produce matrices of the rms distances, rms distances scaled with the
mean distance and the mean distances and matrices with NMR averaged distances (1/r^3 and
1/r^6 averaging). Finally, lists of atom pairs with 1/r^3 and 1/r^6 averaged distance
below the maximum distance (-max, which will default to 0.6 in this case) can be
generated, by default averaging over equivalent hydrogens (all triplets of hydrogens named
*[123]). Additionally a list of equivalent atoms can be supplied (-equiv), each line
containing a set of equivalent atoms specified as residue number and name and atom name;
e.g.:
HB* 3 SER HB1 3 SER HB2
Residue and atom names must exactly match those in the structure file, including case.
Specifying non-sequential atoms is undefined.
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
-equiv [<.dat>] (equiv.dat) (Optional)
Generic data file
Options to specify output files:
-o [<.xvg>] (distrmsd.xvg)
xvgr/xmgr file
-rms [<.xpm>] (rmsdist.xpm) (Optional)
X PixMap compatible matrix file
-scl [<.xpm>] (rmsscale.xpm) (Optional)
X PixMap compatible matrix file
-mean [<.xpm>] (rmsmean.xpm) (Optional)
X PixMap compatible matrix file
-nmr3 [<.xpm>] (nmr3.xpm) (Optional)
X PixMap compatible matrix file
-nmr6 [<.xpm>] (nmr6.xpm) (Optional)
X PixMap compatible matrix file
-noe [<.dat>] (noe.dat) (Optional)
Generic data 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
-nlevels <int> (40)
Discretize RMS in this number of levels
-max <real> (-1)
Maximum level in matrices
-[no]sumh (yes)
Average distance over equivalent hydrogens
-[no]pbc (yes)
Use periodic boundary conditions when computing distances
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