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## tranal_base: reading trajectories

This part is common for all types of trajectory analysis. It reads the first part of the input file and then reads trajectories accordingly. The first part of the input file is written in ``NAMELIST'' format which looks like:

     $TRAJ
     parameter=value(s),
     ...
     $END

```TRAJ`'' is the name of this NAMELIST section.

The following parameters must be defined:

- `NFORM = <format>`

  where `<format>` is one of:

  - `MDYN` - MDynaMix binary trajectory (default)

  - `XMOL` - XMOL trajectory. It is implied, that the commentary (second) line of each configuration is written in the format:

        (char)  <time>  (char-s) BOX:   <box_x> <box_y> <box_z>

    where `(char)` is any character word, `<time>` is time in ,

    `<box_x> <box_y> <box_z>` (following after keyword `BOX`) are the box sizes.

  - `PDBT` - PDB trajectory as generated by ``trajconv'' utility of GROMACS simulation package

  - `DCDT` - DCD trajectories generated by NAMD package

- `FNAME = <file_name>`

  set the base name of the trajectory files. The trajectory must be written as a sequence of files `<file_name>.001` , `<file_name>.002` and so on, the largest possible number being `<file_name>.999` .

- `PATHDB = <value>`

  Directory with molecular description files (.mmol). Default is the current directory (.) .

- `NTYPES = <value>`

  Number of molecule types in the trajectory

- `NAMOL = <name1> [,<name2>,...]`

  `NTYPES` names of molecules. It is supposed that files `<name1>.mmol`, `<name2>.mmol`,... describing the molecules are present in the directory defined by `PATHDB`. Format of .mmol files is the same as for MDynaMix program. For analyzing trajectories generated by other programs, .mmol files are still needed. It is however enough to have only the first section of .mmol files containing names of atoms.

- `NSPEC = <n1>[,<n2>,...]`

  Number of molecules of each type ( `NTYPES` numbers). This parameter is not necessary in MDynaMix binary trajectories.

- `NFBEG = <value>`

  Number of the first trajectory file (integer between 0 and 999)

- `NFEND = <value>`

  Number of the last trajectory file (integer between 0 and 999)

- `IPRINT = <value>`

  Defines how much you see in the intermediate output. The final output with analysis of results does not depend on it. Default value is 5.

-     BOXL = <x-box-size>
      BOYL = <y-box-size>
      BOZL = <z-box-size>

  define the box size if it is not present in the trajectory (implies constant-volume simulation)

- `BREAKM = <value>`

  Defines which break in trajectory (in ps) is allowed to consider the trajectory as continuous. The parameter is used in analysis of time-dependent properties.

- `LVEL = <logical>`

  Accept a logical value. `.true.` signals that the trajectory may contain velocities, which will then be read for the analysis.

- `LXMOL = <logical>`

  Accept a logical value. If .true., rewrite trajectory in XMOL format

  `FXMOL = <name>`

  File name for output XMOL trajectory

- `ISTEP = <value>`

  Specifies that only each `ISTEP`-th configuration from the trajectory is taken for the analysis

- `LBOND = <logical>`

  Accept logical value. If .true., information about bonds is read from .mmol files

- `VFAC = <value>`

  Multiply velocities from the trajectory by the given `<value>`, in order to bring them to Å/fs (the units which are used in the analysis). Default is 1.

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