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]
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DESCRIPTION

23       gmx trjconv can convert trajectory files in many ways:
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25       · from one format to another
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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       · cut  the trajectory in small subtrajectories according to information
42         in an index file. This allows subsequent analysis of the subtrajecto‐
43         ries  that  could,  for example, be the result of a cluster analysis.
44         Use option -sub.  This assumes that the entries in the index file are
45         frame  numbers  and  dumps each group in the index file to a separate
46         trajectory file.
47
48       · select frames within a certain range of a quantity given in  an  .xvg
49         file.
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51       gmx  trjcat  is  better  suited  for  concatenating multiple trajectory
52       files.
53
54       The following formats are supported for input and output:  .xtc,  .trr,
55       .gro,  .g96  and  .pdb.   The  file  formats are detected from the file
56       extension.  The precision of the .xtc output is taken  from  the  input
57       file for .xtc, .gro and .pdb, and from the -ndec option for other input
58       formats. The precision is always taken from -ndec, when this option  is
59       set.  All other formats have fixed precision. .trr output can be single
60       or double precision, depending on the  precision  of  the  gmx  trjconv
61       binary.  Note that velocities are only supported in .trr, .gro and .g96
62       files.
63
64       Option -sep can be used to write every frame to a separate  .gro,  .g96
65       or  .pdb  file.  By  default, all frames all written to one file.  .pdb
66       files with all frames concatenated can be viewed with rasmol -nmrpdb.
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68       It is possible to select part of your trajectory and write it out to  a
69       new  trajectory  file in order to save disk space, e.g. for leaving out
70       the water from a trajectory of a protein  in  water.   ALWAYS  put  the
71       original  trajectory  on  tape!   We recommend to use the portable .xtc
72       format for your analysis to save disk space and to have portable files.
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74       There are two options for fitting the trajectory to a reference  either
75       for  essential  dynamics analysis, etc.  The first option is just plain
76       fitting to a reference structure in  the  structure  file.  The  second
77       option  is  a progressive fit in which the first timeframe is fitted to
78       the reference structure in the structure file to obtain and each subse‐
79       quent  timeframe is fitted to the previously fitted structure. This way
80       a continuous trajectory is generated, which might not be the case  when
81       using  the  regular  fit method, e.g. when your protein undergoes large
82       conformational transitions.
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84       Option -pbc sets the type of periodic boundary condition treatment:
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86          · mol puts the center of mass of molecules in the box, and  requires
87            a run input file to be supplied with -s.
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89          · res puts the center of mass of residues in the box.
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91          · atom puts all the atoms in the box.
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93          · nojump  checks  if  atoms  jump  across the box and then puts them
94            back. This has the effect that all  molecules  will  remain  whole
95            (provided  they were whole in the initial conformation). Note that
96            this ensures a continuous trajectory but molecules may diffuse out
97            of the box. The starting configuration for this procedure is taken
98            from the structure file, if one is supplied, otherwise it  is  the
99            first frame.
100
101          · cluster  clusters  all  the  atoms in the selected index such that
102            they are all closest to the center of mass of the  cluster,  which
103            is  iteratively  updated. Note that this will only give meaningful
104            results if you in fact have a cluster. Luckily that can be checked
105            afterwards using a trajectory viewer. Note also that if your mole‐
106            cules are broken this will not work either.
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108          · whole only makes broken molecules whole.
109
110       Option -ur sets the unit cell representation for options mol,  res  and
111       atom  of  -pbc.  All three options give different results for triclinic
112       boxes and identical results for rectangular boxes.  rect is  the  ordi‐
113       nary  brick  shape.  tric is the triclinic unit cell.  compact puts all
114       atoms at the closest distance from the center of the box. This  can  be
115       useful for visualizing e.g. truncated octahedra or rhombic dodecahedra.
116       The center for options tric and compact is tric (see below), unless the
117       option -boxcenter is set differently.
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119       Option  -center  centers the system in the box. The user can select the
120       group which is used to determine the geometrical center.  Option  -box‐
121       center  sets the location of the center of the box for options -pbc and
122       -center. The center options are: tric: half of the sum of the box  vec‐
123       tors,  rect: half of the box diagonal, zero: zero.  Use option -pbc mol
124       in addition to -center when you want all molecules in the box after the
125       centering.
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127       Option  -box  sets  the size of the new box. This option only works for
128       leading dimensions and is thus generally only  useful  for  rectangular
129       boxes.   If  you  want to modify only some of the dimensions, e.g. when
130       reading from a trajectory, you can use -1  for  those  dimensions  that
131       should  stay  the same It is not always possible to use combinations of
132       -pbc, -fit, -ur and -center to do exactly what you want in one call  to
133       gmx  trjconv.  Consider using multiple calls, and check out the GROMACS
134       website for suggestions.
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136       With -dt, it is possible to reduce the number of frames in the  output.
137       This  option  relies on the accuracy of the times in your input trajec‐
138       tory, so if these are inaccurate use the -timestep option to modify the
139       time  (this  can be done simultaneously). For making smooth movies, the
140       program gmx filter can reduce the number of frames while using low-pass
141       frequency filtering, this reduces aliasing of high frequency motions.
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143       Using  -trunc  gmx  trjconv  can  truncate .trr in place, i.e.  without
144       copying the file. This is useful when a run has crashed during disk I/O
145       (i.e.  full disk), or when two contiguous trajectories must be concate‐
146       nated without having double frames.
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148       Option -dump can be used to extract a frame at  or  near  one  specific
149       time from your trajectory, but only works reliably if the time interval
150       between frames is uniform.
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152       Option -drop reads an .xvg file with times and  values.   When  options
153       -dropunder  and/or  -dropover  are  set,  frames with a value below and
154       above the value of the respective options will not be written.
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OPTIONS

157       Options to specify input files:
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159       -f [<.xtc/.trr/…>] (traj.xtc)
160              Trajectory: xtc trr cpt gro g96 pdb tng
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162       -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
163              Structure+mass(db): tpr gro g96 pdb brk ent
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165       -n [<.ndx>] (index.ndx) (Optional)
166              Index file
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168       -fr [<.ndx>] (frames.ndx) (Optional)
169              Index file
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171       -sub [<.ndx>] (cluster.ndx) (Optional)
172              Index file
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174       -drop [<.xvg>] (drop.xvg) (Optional)
175              xvgr/xmgr file
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177       Options to specify output files:
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179       -o [<.xtc/.trr/…>] (trajout.xtc)
180              Trajectory: xtc trr gro g96 pdb tng
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182       Other options:
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184       -b <time> (0)
185              Time of first frame to read from trajectory (default unit ps)
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187       -e <time> (0)
188              Time of last frame to read from trajectory (default unit ps)
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190       -tu <enum> (ps)
191              Unit for time values: fs, ps, ns, us, ms, s
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193       -[no]w (no)
194              View output .xvg, .xpm, .eps and .pdb files
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196       -xvg <enum> (xmgrace)
197              xvg plot formatting: xmgrace, xmgr, none
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199       -skip <int> (1)
200              Only write every nr-th frame
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202       -dt <time> (0)
203              Only write frame when t MOD dt = first time (ps)
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205       -[no]round (no)
206              Round measurements to nearest picosecond
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208       -dump <time> (-1)
209              Dump frame nearest specified time (ps)
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211       -t0 <time> (0)
212              Starting time (ps) (default: don’t change)
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214       -timestep <time> (0)
215              Change time step between input frames (ps)
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217       -pbc <enum> (none)
218              PBC treatment (see help text for full description):  none,  mol,
219              res, atom, nojump, cluster, whole
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221       -ur <enum> (rect)
222              Unit-cell representation: rect, tric, compact
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224       -[no]center (no)
225              Center atoms in box
226
227       -boxcenter <enum> (tric)
228              Center for -pbc and -center: tric, rect, zero
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230       -box <vector> (0 0 0)
231              Size for new cubic box (default: read from input)
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233       -trans <vector> (0 0 0)
234              All  coordinates  will be translated by trans. This can advanta‐
235              geously be combined with -pbc mol -ur compact.
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237       -shift <vector> (0 0 0)
238              All coordinates will be shifted by framenr*shift
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240       -fit <enum> (none)
241              Fit molecule to ref  structure  in  the  structure  file:  none,
242              rot+trans, rotxy+transxy, translation, transxy, progressive
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244       -ndec <int> (3)
245              Number of decimal places to write to .xtc output
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247       -[no]vel (yes)
248              Read and write velocities if possible
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250       -[no]force (no)
251              Read and write forces if possible
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253       -trunc <time> (-1)
254              Truncate input trajectory file after this time (ps)
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256       -exec <string>
257              Execute  command for every output frame with the frame number as
258              argument
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260       -split <time> (0)
261              Start writing new file when t MOD split = first time (ps)
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263       -[no]sep (no)
264              Write each frame to a separate .gro, .g96 or .pdb file
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266       -nzero <int> (0)
267              If the -sep flag is set, use these many digits for the file num‐
268              bers and prepend zeros as needed
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270       -dropunder <real> (0)
271              Drop all frames below this value
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273       -dropover <real> (0)
274              Drop all frames above this value
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276       -[no]conect (no)
277              Add  conect  records when writing .pdb files. Useful for visual‐
278              ization of non-standard molecules, e.g. coarse grained ones
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SEE ALSO

281       gmx(1)
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283       More    information    about    GROMACS    is    available    at     <‐
284       http://www.gromacs.org/>.
285
287       2019, GROMACS development team
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2922018.7                           May 29, 2019                   GMX-TRJCONV(1)
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