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trjorderMain Table of Contents |
VERSION 4.0_rc1
Mon 22 Sep 2008
| VERSION 4.0_rc1 |
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.
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 refernce group are printed.
| option | filename | type | description |
|---|---|---|---|
| -f | traj.xtc | Input | Trajectory: xtc trr trj gro g96 pdb cpt |
| -s | topol.tpr | Input | Structure+mass(db): tpr tpb tpa gro g96 pdb |
| -n | index.ndx | Input, Opt. | Index file |
| -o | ordered.xtc | Output, Opt. | Trajectory: xtc trr trj gro g96 pdb |
| -nshell | nshell.xvg | Output, Opt. | xvgr/xmgr file |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -nice | int | 19 | Set the nicelevel |
| -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) |
| -[no]xvgr | bool | yes | Add specific codes (legends etc.) in the output xvg files for the xmgrace program |
| -na | int | 3 | Number of atoms in a molecule |
| -da | int | 1 | Atom used for the distance calculation |
| -[no]com | bool | 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 |