1 .TH trjconv 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 trjconv - converts and manipulates trajectory files
9 .BI "\-o" " trajout.xtc "
10 .BI "\-s" " topol.tpr "
11 .BI "\-n" " index.ndx "
12 .BI "\-fr" " frames.ndx "
13 .BI "\-sub" " cluster.ndx "
14 .BI "\-drop" " drop.xvg "
16 .BI "\-[no]version" ""
28 .BI "\-timestep" " time "
32 .BI "\-boxcenter" " enum "
33 .BI "\-box" " vector "
34 .BI "\-trans" " vector "
35 .BI "\-shift" " vector "
40 .BI "\-trunc" " time "
41 .BI "\-exec" " string "
43 .BI "\-split" " time "
46 .BI "\-dropunder" " real "
47 .BI "\-dropover" " real "
50 \&trjconv can convert trajectory files in many ways:
52 \&\fB 1.\fR from one format to another
54 \&\fB 2.\fR select a subset of atoms
56 \&\fB 3.\fR change the periodicity representation
58 \&\fB 4.\fR keep multimeric molecules together
60 \&\fB 5.\fR center atoms in the box
62 \&\fB 6.\fR fit atoms to reference structure
64 \&\fB 7.\fR reduce the number of frames
66 \&\fB 8.\fR change the timestamps of the frames
67 \&(\fB \-t0\fR and \fB \-timestep\fR)
69 \&\fB 9.\fR cut the trajectory in small subtrajectories according
70 \&to information in an index file. This allows subsequent analysis of
71 \&the subtrajectories that could, for example be the result of a
72 \&cluster analysis. Use option \fB \-sub\fR.
73 \&This assumes that the entries in the index file are frame numbers and
74 \&dumps each group in the index file to a separate trajectory file.
76 \&\fB 10.\fR select frames within a certain range of a quantity given
77 \&in an \fB .xvg\fR file.
80 \&The program \fB trjcat\fR can concatenate multiple trajectory files.
84 \&Currently seven formats are supported for input and output:
85 \&\fB .xtc\fR, \fB .trr\fR, \fB .trj\fR, \fB .gro\fR, \fB .g96\fR,
86 \&\fB .pdb\fR and \fB .g87\fR.
87 \&The file formats are detected from the file extension.
88 \&The precision of \fB .xtc\fR and \fB .gro\fR output is taken from the
89 \&input file for \fB .xtc\fR, \fB .gro\fR and \fB .pdb\fR,
90 \&and from the \fB \-ndec\fR option for other input formats. The precision
91 \&is always taken from \fB \-ndec\fR, when this option is set.
92 \&All other formats have fixed precision. \fB .trr\fR and \fB .trj\fR
93 \&output can be single or double precision, depending on the precision
94 \&of the trjconv binary.
95 \&Note that velocities are only supported in
96 \&\fB .trr\fR, \fB .trj\fR, \fB .gro\fR and \fB .g96\fR files.
99 \&Option \fB \-app\fR can be used to
100 \&append output to an existing trajectory file.
101 \&No checks are performed to ensure integrity
102 \&of the resulting combined trajectory file.
105 \&Option \fB \-sep\fR can be used to write every frame to a separate
106 \&.gro, .g96 or .pdb file, default all frames all written to one file.
107 \&\fB .pdb\fR files with all frames concatenated can be viewed with
108 \&\fB rasmol \-nmrpdb\fR.
111 \&It is possible to select part of your trajectory and write it out
112 \&to a new trajectory file in order to save disk space, e.g. for leaving
113 \&out the water from a trajectory of a protein in water.
114 \&\fB ALWAYS\fR put the original trajectory on tape!
115 \&We recommend to use the portable \fB .xtc\fR format for your analysis
116 \&to save disk space and to have portable files.
119 \&There are two options for fitting the trajectory to a reference
120 \&either for essential dynamics analysis or for whatever.
121 \&The first option is just plain fitting to a reference structure
122 \&in the structure file, the second option is a progressive fit
123 \&in which the first timeframe is fitted to the reference structure
124 \&in the structure file to obtain and each subsequent timeframe is
125 \&fitted to the previously fitted structure. This way a continuous
126 \&trajectory is generated, which might not be the case when using the
127 \®ular fit method, e.g. when your protein undergoes large
128 \&conformational transitions.
131 \&Option \fB \-pbc\fR sets the type of periodic boundary condition
134 \&* \fB mol\fR puts the center of mass of molecules in the box.
136 \&* \fB res\fR puts the center of mass of residues in the box.
138 \&* \fB atom\fR puts all the atoms in the box.
140 \&* \fB nojump\fR checks if atoms jump across the box and then puts
141 \&them back. This has the effect that all molecules
142 \&will remain whole (provided they were whole in the initial
143 \&conformation), note that this ensures a continuous trajectory but
144 \&molecules may diffuse out of the box. The starting configuration
145 \&for this procedure is taken from the structure file, if one is
146 \&supplied, otherwise it is the first frame.
148 \&* \fB cluster\fR clusters all the atoms in the selected index
149 \&such that they are all closest to the center of mass of the cluster
150 \&which is iteratively updated. Note that this will only give meaningful
151 \&results if you in fact have a cluster. Luckily that can be checked
152 \&afterwards using a trajectory viewer. Note also that if your molecules
153 \&are broken this will not work either.
155 \&* \fB whole\fR only makes broken molecules whole.
158 \&Option \fB \-ur\fR sets the unit cell representation for options
159 \&\fB mol\fR, \fB res\fR and \fB atom\fR of \fB \-pbc\fR.
160 \&All three options give different results for triclinic boxes and
161 \&identical results for rectangular boxes.
162 \&\fB rect\fR is the ordinary brick shape.
163 \&\fB tric\fR is the triclinic unit cell.
164 \&\fB compact\fR puts all atoms at the closest distance from the center
165 \&of the box. This can be useful for visualizing e.g. truncated
166 \&octahedrons. The center for options \fB tric\fR and \fB compact\fR
167 \&is \fB tric\fR (see below), unless the option \fB \-boxcenter\fR
168 \&is set differently.
171 \&Option \fB \-center\fR centers the system in the box. The user can
172 \&select the group which is used to determine the geometrical center.
173 \&Option \fB \-boxcenter\fR sets the location of the center of the box
174 \&for options \fB \-pbc\fR and \fB \-center\fR. The center options are:
175 \&\fB tric\fR: half of the sum of the box vectors,
176 \&\fB rect\fR: half of the box diagonal,
178 \&Use option \fB \-pbc mol\fR in addition to \fB \-center\fR when you
179 \&want all molecules in the box after the centering.
182 \&With \fB \-dt\fR it is possible to reduce the number of
183 \&frames in the output. This option relies on the accuracy of the times
184 \&in your input trajectory, so if these are inaccurate use the
185 \&\fB \-timestep\fR option to modify the time (this can be done
186 \&simultaneously). For making smooth movies the program \fB g_filter\fR
187 \&can reduce the number of frames while using low\-pass frequency
188 \&filtering, this reduces aliasing of high frequency motions.
191 \&Using \fB \-trunc\fR trjconv can truncate \fB .trj\fR in place, i.e.
192 \&without copying the file. This is useful when a run has crashed
193 \&during disk I/O (one more disk full), or when two contiguous
194 \&trajectories must be concatenated without have double frames.
197 \&\fB trjcat\fR is more suitable for concatenating trajectory files.
200 \&Option \fB \-dump\fR can be used to extract a frame at or near
201 \&one specific time from your trajectory.
204 \&Option \fB \-drop\fR reads an \fB .xvg\fR file with times and values.
205 \&When options \fB \-dropunder\fR and/or \fB \-dropover\fR are set,
206 \&frames with a value below and above the value of the respective options
207 \&will not be written.
209 .BI "\-f" " traj.xtc"
211 Trajectory: xtc trr trj gro g96 pdb cpt
213 .BI "\-o" " trajout.xtc"
215 Trajectory: xtc trr trj gro g96 pdb
217 .BI "\-s" " topol.tpr"
219 Structure+mass(db): tpr tpb tpa gro g96 pdb
221 .BI "\-n" " index.ndx"
225 .BI "\-fr" " frames.ndx"
229 .BI "\-sub" " cluster.ndx"
233 .BI "\-drop" " drop.xvg"
239 Print help info and quit
241 .BI "\-[no]version" "no "
242 Print version info and quit
244 .BI "\-nice" " int" " 19"
247 .BI "\-b" " time" " 0 "
248 First frame (ps) to read from trajectory
250 .BI "\-e" " time" " 0 "
251 Last frame (ps) to read from trajectory
253 .BI "\-tu" " enum" " ps"
254 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR
257 View output xvg, xpm, eps and pdb files
259 .BI "\-xvg" " enum" " xmgrace"
260 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
262 .BI "\-skip" " int" " 1"
263 Only write every nr\-th frame
265 .BI "\-dt" " time" " 0 "
266 Only write frame when t MOD dt = first time (ps)
268 .BI "\-[no]round" "no "
269 Round measurements to nearest picosecond
271 .BI "\-dump" " time" " \-1 "
272 Dump frame nearest specified time (ps)
274 .BI "\-t0" " time" " 0 "
275 Starting time (ps) (default: don't change)
277 .BI "\-timestep" " time" " 0 "
278 Change time step between input frames (ps)
280 .BI "\-pbc" " enum" " none"
281 PBC treatment (see help text for full description): \fB none\fR, \fB mol\fR, \fB res\fR, \fB atom\fR, \fB nojump\fR, \fB cluster\fR or \fB whole\fR
283 .BI "\-ur" " enum" " rect"
284 Unit\-cell representation: \fB rect\fR, \fB tric\fR or \fB compact\fR
286 .BI "\-[no]center" "no "
289 .BI "\-boxcenter" " enum" " tric"
290 Center for \-pbc and \-center: \fB tric\fR, \fB rect\fR or \fB zero\fR
292 .BI "\-box" " vector" " 0 0 0"
293 Size for new cubic box (default: read from input)
295 .BI "\-trans" " vector" " 0 0 0"
296 All coordinates will be translated by trans. This can advantageously be combined with \-pbc mol \-ur compact.
298 .BI "\-shift" " vector" " 0 0 0"
299 All coordinates will be shifted by framenr*shift
301 .BI "\-fit" " enum" " none"
302 Fit molecule to ref structure in the structure file: \fB none\fR, \fB rot+trans\fR, \fB rotxy+transxy\fR, \fB translation\fR, \fB transxy\fR or \fB progressive\fR
304 .BI "\-ndec" " int" " 3"
305 Precision for .xtc and .gro writing in number of decimal places
307 .BI "\-[no]vel" "yes "
308 Read and write velocities if possible
310 .BI "\-[no]force" "no "
311 Read and write forces if possible
313 .BI "\-trunc" " time" " \-1 "
314 Truncate input trj file after this time (ps)
316 .BI "\-exec" " string" " "
317 Execute command for every output frame with the frame number as argument
319 .BI "\-[no]app" "no "
322 .BI "\-split" " time" " 0 "
323 Start writing new file when t MOD split = first time (ps)
325 .BI "\-[no]sep" "no "
326 Write each frame to a separate .gro, .g96 or .pdb file
328 .BI "\-nzero" " int" " 0"
329 Prepend file number in case you use the \-sep flag with this number of zeroes
331 .BI "\-dropunder" " real" " 0 "
332 Drop all frames below this value
334 .BI "\-dropover" " real" " 0 "
335 Drop all frames above this value
337 .BI "\-[no]conect" "no "
338 Add conect records when writing pdb files. Useful for visualization of non\-standard molecules, e.g. coarse grained ones
343 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.