1g_dist(1)                 GROMACS suite, VERSION 4.5                 g_dist(1)
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NAME

6       g_dist  -  calculates  the distances between the centers of mass of two
7       groups
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9       VERSION 4.5
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SYNOPSIS

12       g_dist -f traj.xtc -s topol.tpr -n  index.ndx  -o  dist.xvg  -lt  life‐
13       time.xvg  -[no]h  -[no]version  -nice int -b time -e time -dt time -xvg
14       enum -dist real
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DESCRIPTION

17       g_dist can calculate the distance between the centers of  mass  of  two
18       groups  of atoms as a function of time. The total distance and its x, y
19       and z components are plotted.
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22       Or when  -dist is set, print all the atoms in group 2 that  are  closer
23       than a certain distance to the center of mass of group 1.
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26       With  options   -lt  and   -dist the number of contacts of all atoms in
27       group 2 that are closer than a certain distance to the center  of  mass
28       of  group  1 are plotted as a function of the time that the contact was
29       continously present.
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32       Other programs that calculate distances are  g_mindist and  g_bond.
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FILES

35       -f traj.xtc Input
36        Trajectory: xtc trr trj gro g96 pdb cpt
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38       -s topol.tpr Input
39        Run input file: tpr tpb tpa
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41       -n index.ndx Input, Opt.
42        Index file
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44       -o dist.xvg Output, Opt.
45        xvgr/xmgr file
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47       -lt lifetime.xvg Output, Opt.
48        xvgr/xmgr file
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OTHER OPTIONS

52       -[no]hno
53        Print help info and quit
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55       -[no]versionno
56        Print version info and quit
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58       -nice int 19
59        Set the nicelevel
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61       -b time 0
62        First frame (ps) to read from trajectory
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64       -e time 0
65        Last frame (ps) to read from trajectory
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67       -dt time 0
68        Only use frame when t MOD dt = first time (ps)
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70       -xvg enum xmgrace
71        xvg plot formatting:  xmgrace,  xmgr or  none
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73       -dist real 0
74        Print all atoms in group 2 closer than dist to the center of  mass  of
75       group 1
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SEE ALSO

79       gromacs(7)
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81       More   information  about  GROMACS  is  available  at  <http://www.gro‐
82       macs.org/>.
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86                                Thu 26 Aug 2010                      g_dist(1)