| VERSION 3.2.0 |
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 -or, minimum distances to each residue in the first group are determined and plotted as a function of reisdue number.
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.
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 xml |
-n | index.ndx | Input, Opt. | Index file |
-od | mindist.xvg | Output | xvgr/xmgr file |
-on | numcont.xvg | Output, Opt. | xvgr/xmgr file |
-o | atm-pair.out | Output, Opt. | Generic output file |
-ox | mindist.xtc | Output, Opt. | Generic trajectory: xtc trr trj gro g96 pdb |
-or | mindistres.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 | -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]matrix | bool | no | Calculate half a matrix of group-group distances |
-[no]max | bool | no | Calculate *maximum* distance instead of minimum |
-d | real | 0.6 | Distance for contacts |
-[no]pi | bool | no | Calculate minimum distance with periodic images |
-[no]split | bool | no | Split graph where time is zero |