1 .TH trjconv 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
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 "\-clustercenter" " vector "
35 .BI "\-trans" " vector "
36 .BI "\-shift" " vector "
41 .BI "\-trunc" " time "
42 .BI "\-exec" " string "
44 .BI "\-split" " time "
47 .BI "\-dropunder" " real "
48 .BI "\-dropover" " real "
51 \&\fB trjconv\fR can convert trajectory files in many ways:
53 \&\fB 1.\fR from one format to another
55 \&\fB 2.\fR select a subset of atoms
57 \&\fB 3.\fR change the periodicity representation
59 \&\fB 4.\fR keep multimeric molecules together
61 \&\fB 5.\fR center atoms in the box
63 \&\fB 6.\fR fit atoms to reference structure
65 \&\fB 7.\fR reduce the number of frames
67 \&\fB 8.\fR change the timestamps of the frames
68 \&(\fB \-t0\fR and \fB \-timestep\fR)
70 \&\fB 9.\fR cut the trajectory in small subtrajectories according
71 \&to information in an index file. This allows subsequent analysis of
72 \&the subtrajectories that could, for example, be the result of a
73 \&cluster analysis. Use option \fB \-sub\fR.
74 \&This assumes that the entries in the index file are frame numbers and
75 \&dumps each group in the index file to a separate trajectory file.
77 \&\fB 10.\fR select frames within a certain range of a quantity given
78 \&in an \fB .xvg\fR file.
81 \&The program \fB trjcat\fR is better suited for concatenating multiple trajectory files.
85 \&Currently seven formats are supported for input and output:
86 \&\fB .xtc\fR, \fB .trr\fR, \fB .trj\fR, \fB .gro\fR, \fB .g96\fR,
87 \&\fB .pdb\fR and \fB .g87\fR.
88 \&The file formats are detected from the file extension.
89 \&The precision of \fB .xtc\fR and \fB .gro\fR output is taken from the
90 \&input file for \fB .xtc\fR, \fB .gro\fR and \fB .pdb\fR,
91 \&and from the \fB \-ndec\fR option for other input formats. The precision
92 \&is always taken from \fB \-ndec\fR, when this option is set.
93 \&All other formats have fixed precision. \fB .trr\fR and \fB .trj\fR
94 \&output can be single or double precision, depending on the precision
95 \&of the \fB trjconv\fR binary.
96 \&Note that velocities are only supported in
97 \&\fB .trr\fR, \fB .trj\fR, \fB .gro\fR and \fB .g96\fR files.
100 \&Option \fB \-app\fR can be used to
101 \&append output to an existing trajectory file.
102 \&No checks are performed to ensure integrity
103 \&of the resulting combined trajectory file.
106 \&Option \fB \-sep\fR can be used to write every frame to a separate
107 \&\fB .gro, .g96\fR or \fB .pdb\fR file. By default, all frames all written to one file.
108 \&\fB .pdb\fR files with all frames concatenated can be viewed with
109 \&\fB rasmol \-nmrpdb\fR.
112 \&It is possible to select part of your trajectory and write it out
113 \&to a new trajectory file in order to save disk space, e.g. for leaving
114 \&out the water from a trajectory of a protein in water.
115 \&\fB ALWAYS\fR put the original trajectory on tape!
116 \&We recommend to use the portable \fB .xtc\fR format for your analysis
117 \&to save disk space and to have portable files.
120 \&There are two options for fitting the trajectory to a reference
121 \&either for essential dynamics analysis, etc.
122 \&The first option is just plain fitting to a reference structure
123 \&in the structure file. The second option is a progressive fit
124 \&in which the first timeframe is fitted to the reference structure
125 \&in the structure file to obtain and each subsequent timeframe is
126 \&fitted to the previously fitted structure. This way a continuous
127 \&trajectory is generated, which might not be the case when using the
128 \®ular fit method, e.g. when your protein undergoes large
129 \&conformational transitions.
132 \&Option \fB \-pbc\fR sets the type of periodic boundary condition
135 \&\fB * mol\fR puts the center of mass of molecules in the box,
136 \&and requires a run input file to be supplied with \fB \-s\fR.
138 \&\fB * res\fR puts the center of mass of residues in the box.
140 \&\fB * atom\fR puts all the atoms in the box.
142 \&\fB * nojump\fR checks if atoms jump across the box and then puts
143 \&them back. This has the effect that all molecules
144 \&will remain whole (provided they were whole in the initial
145 \&conformation). \fB Note\fR that this ensures a continuous trajectory but
146 \&molecules may diffuse out of the box. The starting configuration
147 \&for this procedure is taken from the structure file, if one is
148 \&supplied, otherwise it is the first frame.
150 \&\fB * cluster\fR clusters all the atoms in the selected index
151 \&such that they are all closest to the center of mass of the cluster,
152 \&which is iteratively updated. \fB Note\fR that this will only give meaningful
153 \&results if you in fact have a cluster. Luckily that can be checked
154 \&afterwards using a trajectory viewer. Note also that if your molecules
155 \&are broken this will not work either.
157 \&The separate option \fB \-clustercenter\fR can be used to specify an
158 \&approximate center for the cluster. This is useful e.g. if you have
159 \&two big vesicles, and you want to maintain their relative positions.
161 \&\fB * whole\fR only makes broken molecules whole.
164 \&Option \fB \-ur\fR sets the unit cell representation for options
165 \&\fB mol\fR, \fB res\fR and \fB atom\fR of \fB \-pbc\fR.
166 \&All three options give different results for triclinic boxes and
167 \&identical results for rectangular boxes.
168 \&\fB rect\fR is the ordinary brick shape.
169 \&\fB tric\fR is the triclinic unit cell.
170 \&\fB compact\fR puts all atoms at the closest distance from the center
171 \&of the box. This can be useful for visualizing e.g. truncated octahedra
172 \&or rhombic dodecahedra. The center for options \fB tric\fR and \fB compact\fR
173 \&is \fB tric\fR (see below), unless the option \fB \-boxcenter\fR
174 \&is set differently.
177 \&Option \fB \-center\fR centers the system in the box. The user can
178 \&select the group which is used to determine the geometrical center.
179 \&Option \fB \-boxcenter\fR sets the location of the center of the box
180 \&for options \fB \-pbc\fR and \fB \-center\fR. The center options are:
181 \&\fB tric\fR: half of the sum of the box vectors,
182 \&\fB rect\fR: half of the box diagonal,
184 \&Use option \fB \-pbc mol\fR in addition to \fB \-center\fR when you
185 \&want all molecules in the box after the centering.
188 \&It is not always possible to use combinations of \fB \-pbc\fR,
189 \&\fB \-fit\fR, \fB \-ur\fR and \fB \-center\fR to do exactly what
190 \&you want in one call to \fB trjconv\fR. Consider using multiple
191 \&calls, and check out the GROMACS website for suggestions.
194 \&With \fB \-dt\fR, it is possible to reduce the number of
195 \&frames in the output. This option relies on the accuracy of the times
196 \&in your input trajectory, so if these are inaccurate use the
197 \&\fB \-timestep\fR option to modify the time (this can be done
198 \&simultaneously). For making smooth movies, the program \fB g_filter\fR
199 \&can reduce the number of frames while using low\-pass frequency
200 \&filtering, this reduces aliasing of high frequency motions.
203 \&Using \fB \-trunc\fR \fB trjconv\fR can truncate \fB .trj\fR in place, i.e.
204 \&without copying the file. This is useful when a run has crashed
205 \&during disk I/O (i.e. full disk), or when two contiguous
206 \&trajectories must be concatenated without having double frames.
209 \&Option \fB \-dump\fR can be used to extract a frame at or near
210 \&one specific time from your trajectory.
213 \&Option \fB \-drop\fR reads an \fB .xvg\fR file with times and values.
214 \&When options \fB \-dropunder\fR and/or \fB \-dropover\fR are set,
215 \&frames with a value below and above the value of the respective options
216 \&will not be written.
218 .BI "\-f" " traj.xtc"
220 Trajectory: xtc trr trj gro g96 pdb cpt
222 .BI "\-o" " trajout.xtc"
224 Trajectory: xtc trr trj gro g96 pdb
226 .BI "\-s" " topol.tpr"
228 Structure+mass(db): tpr tpb tpa gro g96 pdb
230 .BI "\-n" " index.ndx"
234 .BI "\-fr" " frames.ndx"
238 .BI "\-sub" " cluster.ndx"
242 .BI "\-drop" " drop.xvg"
248 Print help info and quit
250 .BI "\-[no]version" "no "
251 Print version info and quit
253 .BI "\-nice" " int" " 19"
256 .BI "\-b" " time" " 0 "
257 First frame (ps) to read from trajectory
259 .BI "\-e" " time" " 0 "
260 Last frame (ps) to read from trajectory
262 .BI "\-tu" " enum" " ps"
263 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR
266 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
268 .BI "\-xvg" " enum" " xmgrace"
269 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
271 .BI "\-skip" " int" " 1"
272 Only write every nr\-th frame
274 .BI "\-dt" " time" " 0 "
275 Only write frame when t MOD dt = first time (ps)
277 .BI "\-[no]round" "no "
278 Round measurements to nearest picosecond
280 .BI "\-dump" " time" " \-1 "
281 Dump frame nearest specified time (ps)
283 .BI "\-t0" " time" " 0 "
284 Starting time (ps) (default: don't change)
286 .BI "\-timestep" " time" " 0 "
287 Change time step between input frames (ps)
289 .BI "\-pbc" " enum" " none"
290 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
292 .BI "\-ur" " enum" " rect"
293 Unit\-cell representation: \fB rect\fR, \fB tric\fR or \fB compact\fR
295 .BI "\-[no]center" "no "
298 .BI "\-boxcenter" " enum" " tric"
299 Center for \-pbc and \-center: \fB tric\fR, \fB rect\fR or \fB zero\fR
301 .BI "\-box" " vector" " 0 0 0"
302 Size for new cubic box (default: read from input)
304 .BI "\-clustercenter" " vector" " 0 0 0"
305 Optional starting point for pbc cluster option
307 .BI "\-trans" " vector" " 0 0 0"
308 All coordinates will be translated by trans. This can advantageously be combined with \-pbc mol \-ur compact.
310 .BI "\-shift" " vector" " 0 0 0"
311 All coordinates will be shifted by framenr*shift
313 .BI "\-fit" " enum" " none"
314 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
316 .BI "\-ndec" " int" " 3"
317 Precision for .xtc and .gro writing in number of decimal places
319 .BI "\-[no]vel" "yes "
320 Read and write velocities if possible
322 .BI "\-[no]force" "no "
323 Read and write forces if possible
325 .BI "\-trunc" " time" " \-1 "
326 Truncate input trajectory file after this time (ps)
328 .BI "\-exec" " string" " "
329 Execute command for every output frame with the frame number as argument
331 .BI "\-[no]app" "no "
334 .BI "\-split" " time" " 0 "
335 Start writing new file when t MOD split = first time (ps)
337 .BI "\-[no]sep" "no "
338 Write each frame to a separate .gro, .g96 or .pdb file
340 .BI "\-nzero" " int" " 0"
341 If the \-sep flag is set, use these many digits for the file numbers and prepend zeros as needed
343 .BI "\-dropunder" " real" " 0 "
344 Drop all frames below this value
346 .BI "\-dropover" " real" " 0 "
347 Drop all frames above this value
349 .BI "\-[no]conect" "no "
350 Add conect records when writing \fB .pdb\fR files. Useful for visualization of non\-standard molecules, e.g. coarse grained ones
355 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.