6.19 Save the trajectory

VEGA ZZ allows to save/merge a MD trajectory file selecting the frames and changing the output format (trajectory or video stream). It supports both trajectory and video file formats. To show the following dialog window, you must select File Save Trajectory in the main menu:

 

Save trajectory file requester

 

By this file requester, you can choose the file name, the output format, the starting (Start) and the ending (End) trajectory frames and the number of skipped frames (Skip). The Active only option allows to save the active/visible atoms only (see the atom selection). You must remember that if you activate this option, the resulting trajectory isn't compatible with the molecule file used to open the starting one. By this way, you must remove the invisible atoms (Edit Remove Invisible atoms) and save the reference molecule file with the number of atoms compatible with the new trajectory (File Save as ...).
The Swap endian option is available for the CHARMM/NAMD DCD and IFF/RIFF formats only and it changes the byte order (big or little endian) in the resulting binary file, because this format is machine-dependent and it requires a conversion to be readable by specific CPU architectures. VEGA and VEGA ZZ don't require this conversion because they are able to detect the endian of the DCD and IFF/RIFF files and to check the hardware numeric format, applying the endian change if it's required. IFF/RIFF files are written in 64 bit mode in order to avoid the 4 Gb size limit.
The FP precision slider is active only if the Gromacs XTC file format is selected and it can be used to change the floating point precision to store the numbers in the output file (XDRF comtression). The floating point precision is expressed in decimal numbers after the point: e.g. a FP precision of 3 means that the coordinates expressed in Ångström (and not in nanometres) are stored with a precision of 0.001. Remember that higher precisions induce lower compression ratios and consequently larger files.

When you select a file name of an existing trajectory and click the Save button, a window is shown in order to choose the preferred operation:

 

Save  trajectory

 

Clicking Overwrite button, the pre-existent file will be overwritten, clicking Append button, the trajectory will be added to the end to the pre-existent file and clicking Cancel the save process will be aborted. The Append option isn't available when you select a video format.

The following table reports the file trajectory formats written by VEGA ZZ: the first column is the format name, the second one is the file extension, the third one is the type (T = trajectory, V = video),  the fourth indicates if the file is compressed:

Format name Extension Type Compression Notes
CHARMM/NAMD DCD dcd T No Binary file format.
IFF/RIFF iff T No 64 bit binary file format.
Mol2 multi model ml2 T No Text format.
PDB multi model pdb T No Text file format.
Gromacs TRR trr T No Binary file format.
Gromacs XTC xtc T Yes Lossy compression.
AVI video stream avi V Yes It can use several encoding modes.
MPEG-1 video stream mpeg V Yes MPEG-1 encoder.
DVD VOB (Video Object) vob V Yes MPEG-2 encoder.

When you select a video file format, another window is shown  to choose the suitable video encoding options (for more information, click here).