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g_mindistMain Table of Contents |
VERSION 3.1
Thu 28 Feb 2002
| VERSION 3.1 |
g_mindist computes the distance between one group and a number of other groups. Both the minimum distance and the number of contacts within a given distance are written to two separate output files.
With option -pi the minimum distance of a group to its periodic image is plotted. This is useful for checking if a protein has seen its periodic image during a simulation. Only one shift in each direction is considered, giving a total of 26 shifts. It also plots the maximum distance within the group and the lengths of the three box vectors. This option is very slow.
Other programs that calculate distances are g_dist and g_bond.
| option | filename | type | description |
|---|---|---|---|
| -f | traj.xtc | Input | Generic trajectory: xtc trr trj gro g96 pdb |
| -s | topol.tpr | Input, Opt. | Structure+mass(db): tpr tpb tpa gro g96 pdb |
| -n | index.ndx | Input, Opt. | Index file |
| -od | mindist.xvg | Output | xvgr/xmgr file |
| -on | numcont.xvg | Output | xvgr/xmgr file |
| -o | atm-pair.out | Output | Generic output 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) |
| -[no]w | bool | no | View output xvg, xpm, eps and pdb files |
| -[no]matrix | bool | no | Calculate half a matrix of group-group distances |
| -d | real | 0.6 | Distance for contacts |
| -[no]pi | bool | no | Calculate minimum distance with periodic images |