trjorder

Main Table of Contents

VERSION 3.1
Thu 28 Feb 2002


Description

trjorder orders molecules according to the smallest distance to atoms in a reference group. 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. All atoms in the trajectory are written to the output trajectory.

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.

Files

optionfilenametypedescription
-f traj.xtc Input Generic trajectory: xtc trr trj gro g96 pdb
-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-o ordered.xtc Output Generic trajectory: xtc trr trj gro g96 pdb

Other options

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-b time -1 First frame (ps) to read from trajectory
-e time -1 Last frame (ps) to read from trajectory
-dt time -1 Only use frame when t MOD dt = first time (ps)
-na int 3 Number of atoms in a molecule
-da int 1 Atom used for the distance calculation


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