| VERSION 3.0 |
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.
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 |