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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)

       · 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

       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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