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g_trajMain Table of Contents |
VERSION 3.1
Thu 28 Feb 2002
| VERSION 3.1 |
g_traj plots coordinates, velocities, forces and/or the box. With -com the coordinates, velocities and forces are calculated for the center of mass of each group. When -mol is set, the numbers in the index file are interpreted as molecule numbers and the same procedure as with -com is used for each molecule.
Option -ot plots the temperature of each group, provided velocities are present in the trajectory file. No corrections are made for constrained degrees of freedom! This implies -com.
Options -ekt and -ekr plot the translational and rotational kinetic energy of each group, provided velocities are present in the trajectory file. This implies -com.
Options -cv and -cf write the average velocities and average forces as temperature factors to a pdb file with the average coordinates. The temperature factors are scaled such that the maximum is 10. To get the velocities or forces of one frame set both -b and -e to the time of desired frame. When averaging over frames you might need to use the -nojump option to obtain the correct average coordinates.
| option | filename | type | description |
|---|---|---|---|
| -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 |
| -ox | coord.xvg | Output, Opt. | xvgr/xmgr file |
| -ov | veloc.xvg | Output, Opt. | xvgr/xmgr file |
| -of | force.xvg | Output, Opt. | xvgr/xmgr file |
| -ob | box.xvg | Output, Opt. | xvgr/xmgr file |
| -ot | temp.xvg | Output, Opt. | xvgr/xmgr file |
| -ekt | ektrans.xvg | Output, Opt. | xvgr/xmgr file |
| -ekr | ekrot.xvg | Output, Opt. | xvgr/xmgr file |
| -cv | veloc.pdb | Output, Opt. | Protein data bank file |
| -cf | force.pdb | Output, Opt. | Protein data bank file |
| option | type | default | description |
|---|---|---|---|
| -[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) |
| -tu | enum | ps | Time unit: ps, fs, ns, us, ms, s, m or h |
| -[no]w | bool | no | View output xvg, xpm, eps and pdb files |
| -[no]com | bool | no | Plot data for the com of each group |
| -[no]mol | bool | no | Index contains molecule numbers iso atom numbers |
| -[no]nojump | bool | no | Remove jumps of atoms across the box |
| -[no]x | bool | yes | Plot X-component |
| -[no]y | bool | yes | Plot Y-component |
| -[no]z | bool | yes | Plot Z-component |
| -[no]len | bool | no | Plot vector length |