gmx trjconv¶
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
) - select frames within a certain range of a quantity given in an .xvg file.
The option to write subtrajectories (-sub) based on the information obtained from
cluster analysis has been removed from gmx trjconv
and is now part of
[gmx extract-cluster]
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 the .xtc 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.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:
Other options:
-b
<time> (0)- Time of first frame to read from trajectory (default unit ps)
-e
<time> (0)- Time of last frame to read from trajectory (default unit ps)
-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> (xmgrace)- 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)- Number of decimal places to write to .xtc output
-[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