gmx-trjconv(1) GROMACS Manual gmx-trjconv(1)NAMEgmx-trjconv - Convert and manipulates trajectory files
SYNOPSIS
gmx trjconv [-f [<.xtc/.trr/...>]] [-o [<.xtc/.trr/...>]]
[-s [<.tpr/.tpb/...>]] [-n [<.ndx>]] [-fr [<.ndx>]]
[-sub [<.ndx>]] [-drop [<.xvg>]] [-nice <int>]
[-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 for‐
mat to another * select a subset of atoms * change the periodicity rep‐
resentation * 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 tra‐
jectory 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,
.trj, .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 and .trj
output can be single or double precision, depending on the precision of
the gmx trjconv binary. Note that velocities are only supported in
.trr, .trj, .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 orig‐
inal 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 subse‐
quent 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 con‐
figuration 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 vesi‐
cles, 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 -box‐
center 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 vec‐
tors, 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 trajec‐
tory, 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 .trj in place, i.e. without copy‐
ing 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 concate‐
nated 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 and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-o [<.xtc/.trr/...>] (trajout.xtc) (Output)
Trajectory: xtc trr trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-fr [<.ndx>] (frames.ndx) (Input, Optional)
Index file
-sub [<.ndx>] (cluster.ndx) (Input, Optional)
Index file
-drop [<.xvg>] (drop.xvg) (Input, Optional)
xvgr/xmgr file
Other options:
-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: 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 advanta‐
geously 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 visualiza‐
tion of non-standard molecules, e.g. coarse grained ones
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-trjconv(1)
