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gmx-distance(1) | GROMACS Manual | gmx-distance(1) |
NAME¶
gmx-distance - Calculate distances between pairs of positionsSYNOPSIS¶
gmx distance [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]][-n [<.ndx>]] [-oav [<.xvg>]] [-oall [<.xvg>]]
[-oxyz [<.xvg>]] [-oh [<.xvg>]] [-oallstat [<.xvg>]]
[-b <time>] [-e <time>] [-dt <time>] [-tu <enum>]
[-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>]
[-selrpos <enum>] [-select <selection>] [-len <real>]
[-tol <real>] [-binw <real>]
DESCRIPTION¶
gmx distance calculates distances between pairs of positions as a function of time. Each selection specifies an independent set of distances to calculate. Each selection should consist of pairs of positions, and the distances are computed between positions 1-2, 3-4, etc. -oav writes the average distance as a function of time for each selection. -oall writes all the individual distances. -oxyz does the same, but the x, y, and z components of the distance are written instead of the norm. -oh writes a histogram of the distances for each selection. The location of the histogram is set with -len and -tol. Bin width is set with -binw. -oallstat writes out the average and standard deviation for each individual distance, calculated over the frames.OPTIONS¶
Options to specify input and output files: -f [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)Input trajectory or single configuration: xtc trr cpt trj gro g96 pdb tng -s [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)
Input structure: tpr tpb tpa gro g96 pdb brk ent -n [<.ndx>] (index.ndx) (Input, Optional)
Extra index groups -oav [<.xvg>] (distave.xvg) (Output, Optional)
Average distances as function of time -oall [<.xvg>] (dist.xvg) (Output, Optional)
All distances as function of time -oxyz [<.xvg>] (distxyz.xvg) (Output, Optional)
Distance components as function of time -oh [<.xvg>] (disthist.xvg) (Output, Optional)
Histogram of the distances -oallstat [<.xvg>] (diststat.xvg) (Output, Optional)
Statistics for individual distances 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 if t MOD dt == first time (ps) -tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s -xvg <enum> (xmgrace)
Plot formatting: none, xmgrace, xmgr -[no]rmpbc (yes)
Make molecules whole for each frame -[no]pbc (yes)
Use periodic boundary conditions for distance calculation -sf <file>
Provide selections from files -selrpos <enum> (atom)
Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog -select <selection>
Position pairs to calculate distances for -len <real> (0.1)
Mean distance for histogramming -tol <real> (1)
Width of full distribution as fraction of -len -binw <real> (0.001)
Bin width for histogramming
SEE ALSO¶
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.VERSION 5.0.2 |