NAME
trjconv - converts and manipulates trajectory files
VERSION 4.0.1
SYNOPSIS
trjconv -f traj.xtc -o trajout.xtc -s topol.tpr -n index.ndx -fr
frames.ndx -sub cluster.ndx -drop drop.xvg -[no]h -nice int -b time -e
time -tu enum -[no]w -[no]xvgr -skip int -dt time -dump time -t0 time
-timestep time -pbc enum -ur enum -[no]center -boxcenter enum -box
vector -trans vector -shift vector -fit enum -ndec int -[no]vel
-[no]force -trunc time -exec string -[no]app -split time -[no]sep
-nzero int -[no]ter -dropunder real -dropover real
DESCRIPTION
trjconv can convert trajectory files in many ways:
1. from one format to another
2. select a subset of atoms
3. change the periodicity representation
4. keep multimeric molecules together
5. center atoms in the box
6. fit atoms to reference structure
7. reduce the number of frames
8. change the timestamps of the frames ( -t0 and -timestep)
9. cut the trajectory in small subtrajectories according to
information in an index file. This allows subsequent analysis of the
subtrajectories that could, for example be the result of a cluster
analysis. Use option -sub. This assumes that the entries in the index
file are frame numbers and dumps each group in the index file to a
separate trajectory file.
10. select frames within a certain range of a quantity given in an
.xvg file.
The program trjcat can concatenate multiple trajectory files.
Currently seven formats are supported for input and output: .xtc,
.trr, .trj, .gro, .g96, .pdb and .g87. The file formats are
detected from the file extension. The precision of .xtc and .gro
output is taken from the input file for .xtc, .gro and .pdb, and
from the -ndec option for other input formats. The precision is always
taken from -ndec, when this option is set. All other formats have
fixed precision. .trr and .trj output can be single or double
precision, depending on the precision of the trjconv binary. Note that
velocities are only supported in .trr, .trj, .gro and .g96 files.
Option -app can be used to append output to an existing trajectory
file. No checks are performed to ensure integrity of the resulting
combined trajectory file.
Option -sep can be used to write every frame to a seperate .gro, .g96
or .pdb file, default all frames all written to one file. .pdb files
with all frames concatenated can be viewed with rasmol -nmrpdb.
It is possible to select part of your trajectory and write it out to a
new trajectory file in order to save disk space, e.g. for leaving out
the water from a trajectory of a protein in water. ALWAYS put the
original trajectory on tape! We recommend to use the portable .xtc
format for your analysis to save disk space and to have portable files.
There are two options for fitting the trajectory to a reference either
for essential dynamics analysis or for whatever. The first option is
just plain fitting to a reference structure in the structure file, the
second option is a progressive fit in which the first timeframe is
fitted to the reference structure in the structure file to obtain and
each subsequent timeframe is fitted to the previously fitted structure.
This way a continuous trajectory is generated, which might not be the
case when using the regular fit method, e.g. when your protein
undergoes large conformational transitions.
Option -pbc sets the type of periodic boundary condition treatment:
* mol puts the center of mass of molecules in the box.
* res puts the center of mass of residues in the box.
* atom puts all the atoms in the box.
* nojump checks if atoms jump across the box and then puts them back.
This has the effect that all molecules will remain whole (provided they
were whole in the initial conformation), note that this ensures a
continuous trajectory but molecules may diffuse out of the box. The
starting configuration for this procedure is taken from the structure
file, if one is supplied, otherwise it is the first frame.
* cluster clusters all the atoms in the selected index such that they
are all closest to the center of mass of the cluster which is
iteratively updated. Note that this will only give meaningful results
if you in fact have a cluster. Luckily that can be checked afterwards
using a trajectory viewer. Note also that if your molecules are broken
this will not work either.
* whole only makes broken molecules whole.
Option -ur sets the unit cell representation for options mol, res
and atom of -pbc. All three options give different results for
triclinc boxes and identical results for rectangular boxes. rect is
the ordinary brick shape. tric is the triclinic unit cell. compact
puts all atoms at the closest distance from the center of the box. This
can be useful for visualizing e.g. truncated octahedrons. The center
for options tric and compact is tric (see below), unless the option
-boxcenter is set differently.
Option -center centers the system in the box. The user can select the
group which is used to determine the geometrical center. Option
-boxcenter sets the location of the center of the box for options -pbc
and -center. The center options are: tric: half of the sum of the box
vectors, rect: half of the box diagonal, zero: zero. Use option
-pbc mol in addition to -center when you want all molecules in the box
after the centering.
With -dt it is possible to reduce the number of frames in the output.
This option relies on the accuracy of the times in your input
trajectory, so if these are inaccurate use the -timestep option to
modify the time (this can be done simultaneously). For making smooth
movies the program g_filter can reduce the number of frames while
using low-pass frequency filtering, this reduces aliasing of high
frequency motions.
Using -trunc trjconv can truncate .trj in place, i.e. without
copying the file. This is useful when a run has crashed during disk I/O
(one more disk full), or when two contiguous trajectories must be
concatenated without have double frames.
trjcat is more suitable for concatenating trajectory files.
Option -dump can be used to extract a frame at or near one specific
time from your trajectory.
Option -drop reads an .xvg file with times and values. When options
-dropunder and/or -dropover are set, frames with a value below and
above the value of the respective options will not be written.
FILES
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-o trajout.xtc Output
Trajectory: xtc trr trj gro g96 pdb
-s topol.tpr Input, Opt.
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
Index file
-fr frames.ndx Input, Opt.
Index file
-sub cluster.ndx Input, Opt.
Index file
-drop drop.xvg Input, Opt.
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-nice int 19
Set the nicelevel
-b time 0
First frame (ps) to read from trajectory
-e time 0
Last frame (ps) to read from trajectory
-tu enum ps
Time unit: ps, fs, ns, us, ms or s
-[no]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-skip int 1
Only write every nr-th frame
-dt time 0
Only write frame when t MOD dt = first time (ps)
-dump time -1
Dump frame nearest specified time (ps)
-t0 time 0
Starting time (ps) (default: don’t change)
-timestep time 0
Change time step between input frames (ps)
-pbc enum none
PBC treatment (see help text for full description): none, mol, res,
atom, nojump, cluster or whole
-ur enum rect
Unit-cell representation: rect, tric or compact
-[no]centerno
Center atoms in box
-boxcenter enum tric
Center for -pbc and -center: tric, rect or zero
-box vector 0 0 0
Size for new cubic box (default: read from input)
-trans vector 0 0 0
All coordinates will be translated by trans. This can advantageously
be combined with -pbc mol -ur compact.
-shift vector 0 0 0
All coordinates will be shifted by framenr*shift
-fit enum none
Fit molecule to ref structure in the structure file: none,
rot+trans, rotxy+transxy, translation or progressive
-ndec int 3
Precision for .xtc and .gro writing in number of decimal places
-[no]velyes
Read and write velocities if possible
-[no]forceno
Read and write forces if possible
-trunc time -1
Truncate input trj file after this time (ps)
-exec string
Execute command for every output frame with the frame number as
argument
-[no]appno
Append output
-split time 0
Start writing new file when t MOD split = first time (ps)
-[no]sepno
Write each frame to a separate .gro, .g96 or .pdb file
-nzero int 0
Prepend file number in case you use the -sep flag with this number of
zeroes
-[no]terno
Use ’TER’ in pdb file as end of frame in stead of default ’ENDMDL’
-dropunder real 0
Drop all frames below this value
-dropover real 0
Drop all frames above this value
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 trjconv(1)