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g_mindistMain Table of Contents |
VERSION 4.6.7
Fri 29 Aug 2014
| VERSION 4.6.7 |
g_mindist computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from the respective groups) and the number of contacts within a given distance are written to two separate output files. With the -group option a contact of an atom in another group with multiple atoms in the first group is counted as one contact instead of as multiple contacts. With -or, minimum distances to each residue in the first group are determined and plotted as a function of residue 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 | Trajectory: xtc trr trj gro g96 pdb cpt |
| -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, Opt. | xvgr/xmgr file |
| -o | atm-pair.out | Output, Opt. | Generic output file |
| -ox | mindist.xtc | Output, Opt. | 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 |
| -[no]version | bool | no | Print version 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) |
| -tu | enum | ps | Time unit: fs, ps, ns, us, ms or s |
| -[no]w | bool | no | View output .xvg, .xpm, .eps and .pdb files |
| -xvg | enum | xmgrace | xvg plot formatting: xmgrace, xmgr or none |
| -[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]group | bool | no | Count contacts with multiple atoms in the first group as one |
| -[no]pi | bool | no | Calculate minimum distance with periodic images |
| -[no]split | bool | no | Split graph where time is zero |
| -ng | int | 1 | Number of secondary groups to compute distance to a central group |
| -[no]pbc | bool | yes | Take periodic boundary conditions into account |
| -[no]respertime | bool | no | When writing per-residue distances, write distance for each time point |
| -[no]printresname | bool | no | Write residue names |