 |
g_distMain Table of Contents |
VERSION 4.6.1
Tue 5 Mar 2013
| VERSION 4.6.1 |
g_dist can calculate the distance between the centers of mass of two
groups of atoms as a function of time. The total distance and its
Or when -dist is set, print all the atoms in group 2 that are closer than a certain distance to the center of mass of group 1.
With options -lt and -dist the number of contacts of all atoms in group 2 that are closer than a certain distance to the center of mass of group 1 are plotted as a function of the time that the contact was continuously present. The -intra switch enables calculations of intramolecular distances avoiding distance calculation to its periodic images. For a proper function, the molecule in the input trajectory should be whole (e.g. by preprocessing with trjconv -pbc) or a matching topology should be provided. The -intra switch will only give meaningful results for intramolecular and not intermolecular distances.
Other programs that calculate distances are g_mindist and g_bond.
| option | filename | type | description |
|---|---|---|---|
| -f | traj.xtc | Input | Trajectory: xtc trr trj gro g96 pdb cpt |
| -s | topol.tpr | Input | Run input file: tpr tpb tpa |
| -n | index.ndx | Input, Opt. | Index file |
| -o | dist.xvg | Output, Opt. | xvgr/xmgr file |
| -lt | lifetime.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) |
| -xvg | enum | xmgrace | xvg plot formatting: xmgrace, xmgr or none |
| -[no]intra | bool | no | Calculate distances without considering periodic boundaries, e.g. intramolecular. |
| -dist | real | 0 | Print all atoms in group 2 closer than dist to the center of mass of group 1 |