1GMX-CONVERT-TRJ(1)                  GROMACS                 GMX-CONVERT-TRJ(1)
2
3
4

NAME

6       gmx-convert-trj - Converts between different trajectory types
7

SYNOPSIS

9          gmx convert-trj [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
10                       [-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-b <time>]
11                       [-e <time>] [-dt <time>] [-tu <enum>]
12                       [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc]
13                       [-[no]pbc] [-sf <file>] [-selrpos <enum>]
14                       [-select <selection>] [-vel <enum>] [-force <enum>]
15                       [-atoms <enum>] [-precision <int>] [-starttime <time>]
16                       [-timestep <time>] [-box <vector>]
17

DESCRIPTION

19       gmx  convert-trj  converts  trajectory files between different formats.
20       The module supports writing all GROMACS supported file formats from the
21       supported input formats.
22
23       Included  is  also a selection of possible options to modify individual
24       trajectory frames, including options to produce slimmer  output  files.
25       It  is  also possible to replace the particle information stored in the
26       input trajectory with those from a structure file
27
28       The module can also generate subsets of trajectories based on user sup‐
29       plied selections.
30

OPTIONS

32       Options to specify input files:
33
34       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
35              Input  trajectory  or  single configuration: xtc trr cpt gro g96
36              pdb tng
37
38       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
39              Input structure: tpr gro g96 pdb brk ent
40
41       -n [<.ndx>] (index.ndx) (Optional)
42              Extra index groups
43
44       Options to specify output files:
45
46       -o [<.xtc/.trr/...>] (trajout.xtc)
47              Output trajectory: xtc trr cpt gro g96 pdb tng
48
49       Other options:
50
51       -b <time> (0)
52              First frame (ps) to read from trajectory
53
54       -e <time> (0)
55              Last frame (ps) to read from trajectory
56
57       -dt <time> (0)
58              Only use frame if t MOD dt == first time (ps)
59
60       -tu <enum> (ps)
61              Unit for time values: fs, ps, ns, us, ms, s
62
63       -fgroup <selection>
64              Atoms stored in the trajectory file (if not set, assume first  N
65              atoms)
66
67       -xvg <enum> (xmgrace)
68              Plot formatting: xmgrace, xmgr, none
69
70       -[no]rmpbc (yes)
71              Make molecules whole for each frame
72
73       -[no]pbc (yes)
74              Use periodic boundary conditions for distance calculation
75
76       -sf <file>
77              Provide selections from files
78
79       -selrpos <enum> (atom)
80              Selection  reference positions: atom, res_com, res_cog, mol_com,
81              mol_cog,    whole_res_com,     whole_res_cog,     whole_mol_com,
82              whole_mol_cog,    part_res_com,    part_res_cog,   part_mol_com,
83              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
84
85       -select <selection>
86              Selection of particles to write to the file
87
88       -vel <enum> (preserved-if-present)
89              Save velocities from frame  if  possible:  preserved-if-present,
90              always, never
91
92       -force <enum> (preserved-if-present)
93              Save  forces  from  frame if possible: preserved-if-present, al‐
94              ways, never
95
96       -atoms <enum> (preserved-if-present)
97              Decide on providing new atom information from topology or  using
98              current   frame   atom  information:  preserved-if-present,  al‐
99              ways-from-structure, never, always
100
101       -precision <int> (3)
102              Set output precision to custom value
103
104       -starttime <time> (0)
105              Change start time for first frame
106
107       -timestep <time> (0)
108              Change time between different frames
109
110       -box <vector>
111              New diagonal box vector for output frame
112

SEE ALSO

114       gmx(1)
115
116       More    information    about    GROMACS    is    available    at     <‐
117       http://www.gromacs.org/>.
118
120       2022, GROMACS development team
121
122
123
124
1252022.2                           Jun 16, 2022               GMX-CONVERT-TRJ(1)
Impressum