gmx-trjconv - Online in the Cloud

PROGRAM:

NAME

gmx-trjconv - Convert and manipulates trajectory files

SYNOPSIS

gmx trjconv [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-fr [<.ndx>]] [-sub [<.ndx>]] [-drop [<.xvg>]]
[-o [<.xtc/.trr/...>]] [-b <time>] [-e <time>]
[-tu <enum>] [-[no]w] [-xvg <enum>] [-skip <int>]
[-dt <time>] [-[no]round] [-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>] [-split <time>] [-[no]sep]
[-nzero <int>] [-dropunder <real>] [-dropover <real>]
[-[no]conect]

DESCRIPTION

gmx trjconv can convert trajectory files in many ways:

· from one format to another

· select a subset of atoms

· change the periodicity representation

· keep multimeric molecules together

· center atoms in the box

· fit atoms to reference structure

· reduce the number of frames

· change the timestamps of the frames (-t0 and -timestep)

· 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.

· select frames within a certain range of a quantity given in an .xvg file.

gmx trjcat is better suited for concatenating multiple trajectory files.

The following formats are supported for input and output: .xtc, .trr, .gro, .g96 and .pdb.
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 output can be single or double precision,
depending on the precision of the gmx trjconv binary. Note that velocities are only
supported in .trr, .gro and .g96 files.

Option -sep can be used to write every frame to a separate .gro, .g96 or .pdb file. By
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, etc. 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, and requires a run input file to
be supplied with -s.

· 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.

The separate option -clustercenter can be used to specify an approximate center for
the cluster. This is useful e.g. if you have two big vesicles, and you want to
maintain their relative positions.

· 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 triclinic 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 octahedra or rhombic dodecahedra. 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.

Option -box sets the size of the new box. This option only works for leading dimensions
and is thus generally only useful for rectangular boxes. If you want to modify only some
of the dimensions, e.g. when reading from a trajectory, you can use -1 for those
dimensions that should stay the same It is not always possible to use combinations of
-pbc, -fit, -ur and -center to do exactly what you want in one call to gmx trjconv.
Consider using multiple calls, and check out the GROMACS website for suggestions.

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 gmx filter can reduce the number of frames while using low-pass
frequency filtering, this reduces aliasing of high frequency motions.

Using -trunc gmx trjconv can truncate .trr in place, i.e. without copying the file. This
is useful when a run has crashed during disk I/O (i.e. full disk), or when two contiguous
trajectories must be concatenated without having double frames.

Option -dump can be used to extract a frame at or near one specific time from your
trajectory, but only works reliably if the time interval between frames is uniform.

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.

OPTIONS

Options to specify input files:

-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-s [<.tpr/.gro/...>] (topol.tpr) (Optional)
Structure+mass(db): tpr gro g96 pdb brk ent

-n [<.ndx>] (index.ndx) (Optional)
Index file

-fr [<.ndx>] (frames.ndx) (Optional)
Index file

-sub [<.ndx>] (cluster.ndx) (Optional)
Index file

-drop [<.xvg>] (drop.xvg) (Optional)
xvgr/xmgr file

Options to specify output files:

-o [<.xtc/.trr/...>] (trajout.xtc)
Trajectory: xtc trr gro g96 pdb tng

Other options:

-b <time> (0)
First frame (ps) to read from trajectory

-e <time> (0)
Last frame (ps) to read from trajectory

-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files

-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none

-skip <int> (1)
Only write every nr-th frame

-dt <time> (0)
Only write frame when t MOD dt = first time (ps)

-[no]round (no)
Round measurements to nearest picosecond

-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, whole

-ur <enum> (rect)
Unit-cell representation: rect, tric, compact

-[no]center (no)
Center atoms in box

-boxcenter <enum> (tric)
Center for -pbc and -center: tric, rect, 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, transxy, progressive

-ndec <int> (3)
Precision for .xtc and .gro writing in number of decimal places

-[no]vel (yes)
Read and write velocities if possible

-[no]force (no)
Read and write forces if possible

-trunc <time> (-1)
Truncate input trajectory file after this time (ps)

-exec <string>
Execute command for every output frame with the frame number as argument

-split <time> (0)
Start writing new file when t MOD split = first time (ps)

-[no]sep (no)
Write each frame to a separate .gro, .g96 or .pdb file

-nzero <int> (0)
If the -sep flag is set, use these many digits for the file numbers and prepend
zeros as needed

-dropunder <real> (0)
Drop all frames below this value

-dropover <real> (0)
Drop all frames above this value

-[no]conect (no)
Add conect records when writing .pdb files. Useful for visualization of
non-standard molecules, e.g. coarse grained ones

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