GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  GMX-DISTANCE (1)

NAME

gmx-distance - Calculate distances between pairs of positions

CONTENTS

Synopsis
Description
Options
See Also

SYNOPSIS

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/>.

Search for    or go to Top of page |  Section 1 |  Main Index


VERSION 5.0.6 GMX-DISTANCE (1)

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.