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Forcite to MMTK

This converter allows the conversion from a trajectory generated with Materials Studio Forcite module [31] to a MMTK NetCDF trajectory file. Pressing the Forcite to MMTK menubutton, the dialog shown in figure 4.9 will pop up.

Figure 4.9: The Forcite to MMTK converter dialog.

To perform the conversion, the following input fields must be filled:

- XTD/XSD input file
  Format: string
  Default: None
  Description: a XTD or XSD file of the system must be provided for the conversion. This file is necessary to build up the MMTK universe related to the MMTK trajectory. XTD or XSD files are automatically generated during a simulation performed with MaterialsStudio.

- TRJ input file
  Format: string
  Default: None
  Description: the Forcite TRJ file that stores the trajectory frames.

- Subselection:
  Format: integer or Python expression or string
  Default: None
  Description: it can happen that the molecular hierarchy is not correctly set in the XTD/XSD file or that you do not want to include all the atoms of the Discover trajectory into the MMTK trajectory. In that case, it is possible to specify how the system should be organized.

  The format for the Subselection field can be

  - a single integer that specifies the index of the atom to select in the XSD/XTD file,
  - a valid python expression that will generate nesteds list of integers where each list will generate a distinct MMTK AtomCluster made of the atoms whose indexes in the XSD/XTD match the integers of the list. As an example, entering [[1,2,3,5],[10,20,21,23],[90,93]] will consider only atoms 1, 2, 3, 5, 10, 20, 21, 23, 90 and 93 of the XSD/XTD file when creating the MMTK trajectory. Moreover, those atoms will be gathered such as atoms 1, 2, 3 and 5 will be in a fist AtomCluster, atoms 10, 20, 21 and 23 will be in a second AtomCluster and atoms 90 and 93 will be gathered in a third AtomCluster,
  - a string with the following format:
    min_1:max_1:skip_1 sep ... sep min_n:max_n:skip_n
    where sep can be a white space, a comma or a semicolon and each block min_i:max_i:skip_i will specify a distinct MMTK AtomCluster made of atoms whose indexes in the XSD/XTD file ranges from min_i to max_i by jumps of skip_i atoms. For example, entering 2:5:1;20:30:3 will generate a first AtomCluster made of atoms 2,3,4,5 and a second AtomCluster made of atoms 20,23,26 and 29.

- MMTK NetCDF output file
  Format: string
  Default: None
  Description: the name of the MMTK NetCDF trajectory that will be written. Once, a TRJ file has been loaded, a default name for the MMTK NetCDF output file will be proposed. This default name will be file.nc if file.trj is the TRJ trajectory file name.

Next: NAMD to MMTK Up: Trajectory conversion Previous: Discover to MMTK Contents