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gmx-mindist - Online in the Cloud

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This is the command gmx-mindist 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-mindist - Calculate the minimum distance between two groups

SYNOPSIS


gmx mindist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-od [<.xvg>]] [-on [<.xvg>]] [-o [<.out>]]
[-ox [<.xtc/.trr/...>]] [-or [<.xvg>]] [-b <time>]
[-e <time>] [-dt <time>] [-tu <enum>] [-[no]w]
[-xvg <enum>] [-[no]matrix] [-[no]max] [-d <real>]
[-[no]group] [-[no]pi] [-[no]split] [-ng <int>]
[-[no]pbc] [-[no]respertime] [-[no]printresname]

DESCRIPTION


gmx mindist computes the distance between one group and a number of other groups. Both the
minimum distance (between any pair of atoms from the respective groups) and the number of
contacts within a given distance are written to two separate output files. With the
-group option a contact of an atom in another group with multiple atoms in the first group
is counted as one contact instead of as multiple contacts. With -or, minimum distances to
each residue in the first group are determined and plotted as a function of residue
number.

With option -pi the minimum distance of a group to its periodic image is plotted. This is
useful for checking if a protein has seen its periodic image during a simulation. Only one
shift in each direction is considered, giving a total of 26 shifts. It also plots the
maximum distance within the group and the lengths of the three box vectors.

Also gmx distance and gmx pairdist calculate distances.

OPTIONS


Options to specify input files:

-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-s [<.tpr/.gro/...>] (topol.tpr) (Optional)
Structure+mass(db): tpr gro g96 pdb brk ent

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

Options to specify output files:

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

-on [<.xvg>] (numcont.xvg) (Optional)
xvgr/xmgr file

-o [<.out>] (atm-pair.out) (Optional)
Generic output file

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

-or [<.xvg>] (mindistres.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)

-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files

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

-[no]matrix (no)
Calculate half a matrix of group-group distances

-[no]max (no)
Calculate maximum distance instead of minimum

-d <real> (0.6)
Distance for contacts

-[no]group (no)
Count contacts with multiple atoms in the first group as one

-[no]pi (no)
Calculate minimum distance with periodic images

-[no]split (no)
Split graph where time is zero

-ng <int> (1)
Number of secondary groups to compute distance to a central group

-[no]pbc (yes)
Take periodic boundary conditions into account

-[no]respertime (no)
When writing per-residue distances, write distance for each time point

-[no]printresname (no)
Write residue names

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