1GMX-TRJCONV(1)                      GROMACS                     GMX-TRJCONV(1)
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NAME

6       gmx-trjconv - Convert and manipulates trajectory files
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SYNOPSIS

9          gmx trjconv [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                      [-fr [<.ndx>]] [-sub [<.ndx>]] [-drop [<.xvg>]]
11                      [-o [<.xtc/.trr/...>]] [-b <time>] [-e <time>]
12                      [-tu <enum>] [-[no]w] [-xvg <enum>] [-skip <int>]
13                      [-dt <time>] [-[no]round] [-dump <time>] [-t0 <time>]
14                      [-timestep <time>] [-pbc <enum>] [-ur <enum>]
15                      [-[no]center] [-boxcenter <enum>] [-box <vector>]
16                      [-trans <vector>] [-shift <vector>] [-fit <enum>]
17                      [-ndec <int>] [-[no]vel] [-[no]force] [-trunc <time>]
18                      [-exec <string>] [-split <time>] [-[no]sep]
19                      [-nzero <int>] [-dropunder <real>] [-dropover <real>]
20                      [-[no]conect]
21

DESCRIPTION

23       gmx trjconv can convert trajectory files in many ways:
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25       • from one format to another
26
27       • select a subset of atoms
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29       • change the periodicity representation
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31       • keep multimeric molecules together
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33       • center atoms in the box
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35       • fit atoms to reference structure
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37       • reduce the number of frames
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39       • change the timestamps of the frames (-t0 and -timestep)
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41       • select  frames  within a certain range of a quantity given in an .xvg
42         file.
43
44       The option to write subtrajectories (-sub) based on the information ob‐
45       tained  from  cluster analysis has been removed from gmx trjconv and is
46       now part of [gmx extract-cluster]
47
48       gmx trjcat is  better  suited  for  concatenating  multiple  trajectory
49       files.
50
51       The  following  formats are supported for input and output: .xtc, .trr,
52       .gro, .g96, .pdb and .tng.  The file formats are detected from the file
53       extension.   The  precision  of the .xtc output is taken from the input
54       file for .xtc, .gro and .pdb, and from the -ndec option for other input
55       formats.  The precision is always taken from -ndec, when this option is
56       set.  All other formats have fixed precision. .trr output can be single
57       or  double precision, depending on the precision of the gmx trjconv bi‐
58       nary.  Note that velocities are only supported in .trr, .tng, .gro  and
59       .g96 files.
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61       Option  -sep  can be used to write every frame to a separate .gro, .g96
62       or .pdb file. By default, all frames all written  to  one  file.   .pdb
63       files with all frames concatenated can be viewed with rasmol -nmrpdb.
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65       It  is possible to select part of your trajectory and write it out to a
66       new trajectory file in order to save disk space, e.g. for  leaving  out
67       the  water  from  a  trajectory  of a protein in water.  ALWAYS put the
68       original trajectory on tape!  We recommend to  use  the  portable  .xtc
69       format for your analysis to save disk space and to have portable files.
70       When writing .tng output the file will contain one molecule type of the
71       correct  count  if the selection name matches the molecule name and the
72       selected atoms match all atoms of that molecule.  Otherwise  the  whole
73       selection will be treated as one single molecule containing all the se‐
74       lected atoms.
75
76       There are two options for fitting the trajectory to a reference  either
77       for  essential  dynamics analysis, etc.  The first option is just plain
78       fitting to a reference structure in the structure file. The second  op‐
79       tion is a progressive fit in which the first timeframe is fitted to the
80       reference structure in the structure file to obtain and each subsequent
81       timeframe is fitted to the previously fitted structure. This way a con‐
82       tinuous trajectory is generated, which might not be the case when using
83       the  regular fit method, e.g. when your protein undergoes large confor‐
84       mational transitions.
85
86       Option -pbc sets the type of periodic boundary condition treatment:
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88mol puts the center of mass of molecules in the box, and  requires
89            a run input file to be supplied with -s.
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91res puts the center of mass of residues in the box.
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93atom puts all the atoms in the box.
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95nojump  checks  if  atoms  jump  across the box and then puts them
96            back. This has the effect that all  molecules  will  remain  whole
97            (provided  they were whole in the initial conformation). Note that
98            this ensures a continuous trajectory but molecules may diffuse out
99            of the box. The starting configuration for this procedure is taken
100            from the structure file, if one is supplied, otherwise it  is  the
101            first frame.
102
103cluster  clusters  all  the  atoms in the selected index such that
104            they are all closest to the center of mass of the  cluster,  which
105            is  iteratively  updated. Note that this will only give meaningful
106            results if you in fact have a cluster. Luckily that can be checked
107            afterwards using a trajectory viewer. Note also that if your mole‐
108            cules are broken this will not work either.
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110whole only makes broken molecules whole.
111
112       Option -ur sets the unit cell representation for options mol,  res  and
113       atom  of  -pbc.  All three options give different results for triclinic
114       boxes and identical results for rectangular boxes.  rect is  the  ordi‐
115       nary  brick  shape.  tric is the triclinic unit cell.  compact puts all
116       atoms at the closest distance from the center of the box. This  can  be
117       useful for visualizing e.g. truncated octahedra or rhombic dodecahedra.
118       The center for options tric and compact is tric (see below), unless the
119       option -boxcenter is set differently.
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121       Option  -center  centers the system in the box. The user can select the
122       group which is used to determine the geometrical center.  Option  -box‐
123       center  sets the location of the center of the box for options -pbc and
124       -center. The center options are: tric: half of the sum of the box  vec‐
125       tors,  rect: half of the box diagonal, zero: zero.  Use option -pbc mol
126       in addition to -center when you want all molecules in the box after the
127       centering.
128
129       Option  -box  sets  the size of the new box. This option only works for
130       leading dimensions and is thus generally only  useful  for  rectangular
131       boxes.   If  you  want to modify only some of the dimensions, e.g. when
132       reading from a trajectory, you can use -1  for  those  dimensions  that
133       should  stay  the same It is not always possible to use combinations of
134       -pbc, -fit, -ur and -center to do exactly what you want in one call  to
135       gmx  trjconv.  Consider using multiple calls, and check out the GROMACS
136       website for suggestions.
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138       With -dt, it is possible to reduce the number of frames in the  output.
139       This  option  relies on the accuracy of the times in your input trajec‐
140       tory, so if these are inaccurate use the -timestep option to modify the
141       time  (this  can be done simultaneously). For making smooth movies, the
142       program gmx filter can reduce the number of frames while using low-pass
143       frequency filtering, this reduces aliasing of high frequency motions.
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145       Using  -trunc  gmx  trjconv  can  truncate .trr in place, i.e.  without
146       copying the file. This is useful when a run has crashed during disk I/O
147       (i.e.  full disk), or when two contiguous trajectories must be concate‐
148       nated without having double frames.
149
150       Option -dump can be used to extract a frame at  or  near  one  specific
151       time  from  your trajectory. If the frames in the trajectory are not in
152       temporal order, the result is unspecified.
153
154       Option -drop reads an .xvg file with times and  values.   When  options
155       -dropunder  and/or  -dropover  are  set,  frames with a value below and
156       above the value of the respective options will not be written.
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OPTIONS

159       Options to specify input files:
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161       -f [<.xtc/.trr/...>] (traj.xtc)
162              Trajectory: xtc trr cpt gro g96 pdb tng
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164       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
165              Structure+mass(db): tpr gro g96 pdb brk ent
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167       -n [<.ndx>] (index.ndx) (Optional)
168              Index file
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170       -fr [<.ndx>] (frames.ndx) (Optional)
171              Index file
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173       -sub [<.ndx>] (cluster.ndx) (Optional)
174              Index file
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176       -drop [<.xvg>] (drop.xvg) (Optional)
177              xvgr/xmgr file
178
179       Options to specify output files:
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181       -o [<.xtc/.trr/...>] (trajout.xtc)
182              Trajectory: xtc trr gro g96 pdb tng
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184       Other options:
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186       -b <time> (0)
187              Time of first frame to read from trajectory (default unit ps)
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189       -e <time> (0)
190              Time of last frame to read from trajectory (default unit ps)
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192       -tu <enum> (ps)
193              Unit for time values: fs, ps, ns, us, ms, s
194
195       -[no]w (no)
196              View output .xvg, .xpm, .eps and .pdb files
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198       -xvg <enum> (xmgrace)
199              xvg plot formatting: xmgrace, xmgr, none
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201       -skip <int> (1)
202              Only write every nr-th frame
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204       -dt <time> (0)
205              Only write frame when t MOD dt = first time (ps)
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207       -[no]round (no)
208              Round measurements to nearest picosecond
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210       -dump <time> (-1)
211              Dump frame nearest specified time (ps)
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213       -t0 <time> (0)
214              Starting time (ps) (default: don't change)
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216       -timestep <time> (0)
217              Change time step between input frames (ps)
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219       -pbc <enum> (none)
220              PBC treatment (see help text for full description):  none,  mol,
221              res, atom, nojump, cluster, whole
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223       -ur <enum> (rect)
224              Unit-cell representation: rect, tric, compact
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226       -[no]center (no)
227              Center atoms in box
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229       -boxcenter <enum> (tric)
230              Center for -pbc and -center: tric, rect, zero
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232       -box <vector> (0 0 0)
233              Size for new cubic box (default: read from input)
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235       -trans <vector> (0 0 0)
236              All  coordinates  will be translated by trans. This can advanta‐
237              geously be combined with -pbc mol -ur compact.
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239       -shift <vector> (0 0 0)
240              All coordinates will be shifted by framenr*shift
241
242       -fit <enum> (none)
243              Fit molecule to ref  structure  in  the  structure  file:  none,
244              rot+trans, rotxy+transxy, translation, transxy, progressive
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246       -ndec <int> (3)
247              Number of decimal places to write to .xtc output
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249       -[no]vel (yes)
250              Read and write velocities if possible
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252       -[no]force (no)
253              Read and write forces if possible
254
255       -trunc <time> (-1)
256              Truncate input trajectory file after this time (ps)
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258       -exec <string>
259              Execute  command for every output frame with the frame number as
260              argument
261
262       -split <time> (0)
263              Start writing new file when t MOD split = first time (ps)
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265       -[no]sep (no)
266              Write each frame to a separate .gro, .g96 or .pdb file
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268       -nzero <int> (0)
269              If the -sep flag is set, use these many digits for the file num‐
270              bers and prepend zeros as needed
271
272       -dropunder <real> (0)
273              Drop all frames below this value
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275       -dropover <real> (0)
276              Drop all frames above this value
277
278       -[no]conect (no)
279              Add CONECT PDB records when writing .pdb files. Useful for visu‐
280              alization of non-standard molecules, e.g. coarse grained ones
281

SEE ALSO

283       gmx(1)
284
285       More    information    about    GROMACS    is    available    at     <‐
286       http://www.gromacs.org/>.
287
289       2022, GROMACS development team
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2942022.3                           Sep 02, 2022                   GMX-TRJCONV(1)
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