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gmx-trjorder - Online in the Cloud

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This is the command gmx-trjorder 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-trjorder - Order molecules according to their distance to a group

SYNOPSIS


gmx trjorder [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-o [<.xtc/.trr/...>]] [-nshell [<.xvg>]] [-b <time>]
[-e <time>] [-dt <time>] [-xvg <enum>] [-na <int>]
[-da <int>] [-[no]com] [-r <real>] [-[no]z]

DESCRIPTION


gmx trjorder orders molecules according to the smallest distance to atoms in a reference
group or on z-coordinate (with option -z). With distance ordering, it will ask for a
group of reference atoms and a group of molecules. For each frame of the trajectory the
selected molecules will be reordered according to the shortest distance between atom
number -da in the molecule and all the atoms in the reference group. The center of mass of
the molecules can be used instead of a reference atom by setting -da to 0. All atoms in
the trajectory are written to the output trajectory.

gmx trjorder can be useful for e.g. analyzing the n waters closest to a protein. In that
case the reference group would be the protein and the group of molecules would consist of
all the water atoms. When an index group of the first n waters is made, the ordered
trajectory can be used with any GROMACS program to analyze the n closest waters.

If the output file is a .pdb file, the distance to the reference target will be stored in
the B-factor field in order to color with e.g. Rasmol.

With option -nshell the number of molecules within a shell of radius -r around the
reference group are printed.

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

Options to specify output files:

-o [<.xtc/.trr/...>] (ordered.xtc) (Optional)
Trajectory: xtc trr gro g96 pdb tng

-nshell [<.xvg>] (nshell.xvg) (Optional)
xvgr/xmgr 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)

-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none

-na <int> (3)
Number of atoms in a molecule

-da <int> (1)
Atom used for the distance calculation, 0 is COM

-[no]com (no)
Use the distance to the center of mass of the reference group

-r <real> (0)
Cutoff used for the distance calculation when computing the number of molecules in
a shell around e.g. a protein

-[no]z (no)
Order molecules on z-coordinate

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