1trjconv(1) GROMACS suite, VERSION 4.5 trjconv(1)
2
6 trjconv - converts and manipulates trajectory files
7 VERSION 4.5
9
11 trjconv -f traj.xtc -o trajout.xtc -s topol.tpr -n index.ndx -fr
12 frames.ndx -sub cluster.ndx -drop drop.xvg -[no]h -[no]version -nice
13 int -b time -e time -tu enum -[no]w -xvg enum -skip int -dt time
14 -[no]round -dump time -t0 time -timestep time -pbc enum -ur enum
15 -[no]center -boxcenter enum -box vector -trans vector -shift vector
16 -fit enum -ndec int -[no]vel -[no]force -trunc time -exec string
17 -[no]app -split time -[no]sep -nzero int -dropunder real -dropover real
18 -[no]conect
19
21 trjconv can convert trajectory files in many ways:
22 1. from one format to another
24 2. select a subset of atoms
26 3. change the periodicity representation
28 4. keep multimeric molecules together
30 5. center atoms in the box
32 6. fit atoms to reference structure
34 7. reduce the number of frames
36 8. change the timestamps of the frames ( -t0 and -timestep)
38 9. cut the trajectory in small subtrajectories according to informa‐
40 tion in an index file. This allows subsequent analysis of the subtra‐
41 jectories that could, for example be the result of a cluster analysis.
42 Use option -sub. This assumes that the entries in the index file are
43 frame numbers and dumps each group in the index file to a separate tra‐
44 jectory file.
45 10. select frames within a certain range of a quantity given in an
47 .xvg file.
48 The program trjcat can concatenate multiple trajectory files.
51 Currently seven formats are supported for input and output: .xtc,
54 .trr, .trj, .gro, .g96, .pdb and .g87. The file formats are
55 detected from the file extension. The precision of .xtc and .gro
56 output is taken from the input file for .xtc, .gro and .pdb, and
57 from the -ndec option for other input formats. The precision is always
58 taken from -ndec, when this option is set. All other formats have
59 fixed precision. .trr and .trj output can be single or double preci‐
60 sion, depending on the precision of the trjconv binary. Note that
61 velocities are only supported in .trr, .trj, .gro and .g96 files.
62 Option -app can be used to append output to an existing trajectory
65 file. No checks are performed to ensure integrity of the resulting
66 combined trajectory file.
67 Option -sep can be used to write every frame to a separate .gro, .g96
70 or .pdb file, default all frames all written to one file. .pdb files
71 with all frames concatenated can be viewed with rasmol -nmrpdb.
72 It is possible to select part of your trajectory and write it out to a
75 new trajectory file in order to save disk space, e.g. for leaving out
76 the water from a trajectory of a protein in water. ALWAYS put the
77 original trajectory on tape! We recommend to use the portable .xtc
78 format for your analysis to save disk space and to have portable files.
79 There are two options for fitting the trajectory to a reference either
82 for essential dynamics analysis or for whatever. The first option is
83 just plain fitting to a reference structure in the structure file, the
84 second option is a progressive fit in which the first timeframe is fit‐
85 ted to the reference structure in the structure file to obtain and each
86 subsequent timeframe is fitted to the previously fitted structure. This
87 way a continuous trajectory is generated, which might not be the case
88 when using the regular fit method, e.g. when your protein undergoes
89 large conformational transitions.
90 Option -pbc sets the type of periodic boundary condition treatment:
93 * mol puts the center of mass of molecules in the box.
95 * res puts the center of mass of residues in the box.
97 * atom puts all the atoms in the box.
99 * nojump checks if atoms jump across the box and then puts them back.
101 This has the effect that all molecules will remain whole (provided they
102 were whole in the initial conformation), note that this ensures a con‐
103 tinuous trajectory but molecules may diffuse out of the box. The start‐
104 ing configuration for this procedure is taken from the structure file,
105 if one is supplied, otherwise it is the first frame.
106 * cluster clusters all the atoms in the selected index such that they
108 are all closest to the center of mass of the cluster which is itera‐
109 tively updated. Note that this will only give meaningful results if you
110 in fact have a cluster. Luckily that can be checked afterwards using a
111 trajectory viewer. Note also that if your molecules are broken this
112 will not work either.
113 * whole only makes broken molecules whole.
115 Option -ur sets the unit cell representation for options mol, res
118 and atom of -pbc. All three options give different results for tri‐
119 clinic boxes and identical results for rectangular boxes. rect is the
120 ordinary brick shape. tric is the triclinic unit cell. compact puts
121 all atoms at the closest distance from the center of the box. This can
122 be useful for visualizing e.g. truncated octahedrons. The center for
123 options tric and compact is tric (see below), unless the option
124 -boxcenter is set differently.
125 Option -center centers the system in the box. The user can select the
128 group which is used to determine the geometrical center. Option -box‐
129 center sets the location of the center of the box for options -pbc and
130 -center. The center options are: tric: half of the sum of the box vec‐
131 tors, rect: half of the box diagonal, zero: zero. Use option -pbc
132 mol in addition to -center when you want all molecules in the box
133 after the centering.
134 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
139 the time (this can be done simultaneously). For making smooth movies
140 the program g_filter can reduce the number of frames while using
141 low-pass frequency filtering, this reduces aliasing of high frequency
142 motions.
143 Using -trunc trjconv can truncate .trj in place, i.e. without copy‐
146 ing the file. This is useful when a run has crashed during disk I/O
147 (one more disk full), or when two contiguous trajectories must be con‐
148 catenated without have double frames.
149 trjcat is more suitable for concatenating trajectory files.
152 Option -dump can be used to extract a frame at or near one specific
155 time from your trajectory.
156 Option -drop reads an .xvg file with times and values. When options
159 -dropunder and/or -dropover are set, frames with a value below and
160 above the value of the respective options will not be written.
161
163 -f traj.xtc Input
164 Trajectory: xtc trr trj gro g96 pdb cpt
165 -o trajout.xtc Output
167 Trajectory: xtc trr trj gro g96 pdb
168 -s topol.tpr Input, Opt.
170 Structure+mass(db): tpr tpb tpa gro g96 pdb
171 -n index.ndx Input, Opt.
173 Index file
174 -fr frames.ndx Input, Opt.
176 Index file
177 -sub cluster.ndx Input, Opt.
179 Index file
180 -drop drop.xvg Input, Opt.
182 xvgr/xmgr file
183
186 -[no]hno
187 Print help info and quit
188 -[no]versionno
190 Print version info and quit
191 -nice int 19
193 Set the nicelevel
194 -b time 0
196 First frame (ps) to read from trajectory
197 -e time 0
199 Last frame (ps) to read from trajectory
200 -tu enum ps
202 Time unit: fs, ps, ns, us, ms or s
203 -[no]wno
205 View output xvg, xpm, eps and pdb files
206 -xvg enum xmgrace
208 xvg plot formatting: xmgrace, xmgr or none
209 -skip int 1
211 Only write every nr-th frame
212 -dt time 0
214 Only write frame when t MOD dt = first time (ps)
215 -[no]roundno
217 Round measurements to nearest picosecond
218 -dump time -1
220 Dump frame nearest specified time (ps)
221 -t0 time 0
223 Starting time (ps) (default: don't change)
224 -timestep time 0
226 Change time step between input frames (ps)
227 -pbc enum none
229 PBC treatment (see help text for full description): none, mol, res,
230 atom, nojump, cluster or whole
231 -ur enum rect
233 Unit-cell representation: rect, tric or compact
234 -[no]centerno
236 Center atoms in box
237 -boxcenter enum tric
239 Center for -pbc and -center: tric, rect or zero
240 -box vector 0 0 0
242 Size for new cubic box (default: read from input)
243 -trans vector 0 0 0
245 All coordinates will be translated by trans. This can advantageously
246 be combined with -pbc mol -ur compact.
247 -shift vector 0 0 0
249 All coordinates will be shifted by framenr*shift
250 -fit enum none
252 Fit molecule to ref structure in the structure file: none,
253 rot+trans, rotxy+transxy, translation, transxy or progressive
254 -ndec int 3
256 Precision for .xtc and .gro writing in number of decimal places
257 -[no]velyes
259 Read and write velocities if possible
260 -[no]forceno
262 Read and write forces if possible
263 -trunc time -1
265 Truncate input trj file after this time (ps)
266 -exec string
268 Execute command for every output frame with the frame number as argu‐
269 ment
270 -[no]appno
272 Append output
273 -split time 0
275 Start writing new file when t MOD split = first time (ps)
276 -[no]sepno
278 Write each frame to a separate .gro, .g96 or .pdb file
279 -nzero int 0
281 Prepend file number in case you use the -sep flag with this number of
282 zeroes
283 -dropunder real 0
285 Drop all frames below this value
286 -dropover real 0
288 Drop all frames above this value
289 -[no]conectno
291 Add conect records when writing pdb files. Useful for visualization of
292 non-standard molecules, e.g. coarse grained ones
293
296 gromacs(7)
297 More information about GROMACS is available at <http://www.gro‐
299 macs.org/>.
300 Thu 26 Aug 2010 trjconv(1)