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       gmx-trjconv - Convert and manipulates trajectory files


          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>]


       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 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

       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 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)
              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



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