Provided by: gromacs-data_4.6.5-1build1_all bug


       trjconv - converts and manipulates trajectory files

       VERSION 4.6.5


       trjconv  -f  traj.xtc  -o  trajout.xtc  -s  topol.tpr  -n  index.ndx  -fr  frames.ndx -sub
       cluster.ndx -drop drop.xvg -[no]h -[no]version -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 -clustercenter vector  -trans  vector  -shift
       vector  -fit  enum  -ndec int -[no]vel -[no]force -trunc time -exec string -[no]app -split
       time -[no]sep -nzero int -dropunder real -dropover real -[no]conect


        trjconv can convert trajectory files in many ways:

        1. from one format to another

        2. select a subset of atoms

        3. change the periodicity representation

        4. keep multimeric molecules together

        5. center atoms in the box

        6. fit atoms to reference structure

        7. reduce the number of frames

        8. change the timestamps of the frames ( -t0 and  -timestep)

        9. 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.

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

       The program  trjcat is better suited for concatenating multiple trajectory files.

       Currently seven formats are supported for input and output:  .xtc,   .trr,   .trj,   .gro,
       .g96,    .pdb  and   .g87.   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  trjconv
       binary.  Note that velocities are only supported in  .trr,  .trj,  .gro and  .g96 files.

       Option  -app can be used to append output to an existing trajectory file.  No  checks  are
       performed to ensure integrity of the resulting combined trajectory file.

       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

       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.

       It  is  not  always  possible to use combinations of  -pbc,  -fit,  -ur and  -center to do
       exactly what you want in one call to  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  g_filter can  reduce  the  number  of  frames  while  using  low-pass
       frequency filtering, this reduces aliasing of high frequency motions.

       Using   -trunc   trjconv can truncate  .trj 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

       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.


       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -o trajout.xtc Output
        Trajectory: xtc trr trj gro g96 pdb

       -s topol.tpr Input, Opt.
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -fr frames.ndx Input, Opt.
        Index file

       -sub cluster.ndx Input, Opt.
        Index file

       -drop drop.xvg Input, Opt.
        xvgr/xmgr file


        Print help info and quit

        Print version info and quit

       -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 or  s

        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -skip int 1
        Only write every nr-th frame

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

        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 or  whole

       -ur enum rect
        Unit-cell representation:  rect,  tric or  compact

        Center atoms in box

       -boxcenter enum tric
        Center for -pbc and -center:  tric,  rect or  zero

       -box vector 0 0 0
        Size for new cubic box (default: read from input)

       -clustercenter vector 0 0 0
        Optional starting point for pbc cluster option

       -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 or  progressive

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

        Read and write velocities if possible

        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

        Append output

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

        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

       -dropunder real 0
        Drop all frames below this value

       -dropover real 0
        Drop all frames above this value

        Add conect records when writing  .pdb files. Useful  for  visualization  of  non-standard
       molecules, e.g. coarse grained ones



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                               trjconv(1)