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DL_POLY to MMTK

This converter allows the conversion from a trajectory generated with DL_POLY [28] to a MMTK NetCDF trajectory. Pressing the DL_POLY to MMTK menubutton, the dialog shown in figure 4.6 will pop up.

Figure 4.6: The DL_POLY to MMTK converter dialog.

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

- FIELD input file
  Format: string
  Default: None
  Description: the DL_POLY FIELD file that stores the informations about the system. This file is necessary to build up the MMTK universe related to the MMTK trajectory.

- HISTORY input file
  Format: string
  Default: None
  Description: the DL_POLY HISTORY file that stores the trajectory frames.

- Special atoms
  Format: string
  Default: None
  Description: nMOLDYN will create the MMTK universe with the atom names specified in the FIELD file. By default, nMOLDYN will interpret these names directly as if they were a chemical symbol. If this fails, nMOLDYN will remove the last character until it corresponds to a known chemical symbol. For example, an atom defined in the FIELD file as CB, will first be interpreted as an atom of chemical symbol CB. As it does not exist, nMOLDYN will interpret it as an atom of chemical symbol C, namely a carbon atom. Usig htis procedure, it can happen that some atom names can be misunderstood or event not understood at all by MMTKAs an example, the figure 4.7 shows the example of a FIELD file where one carbon atom specification (the one in red in the figure) will be misinterpreted as a cesium atom.

  Figure 4.7: Example of a DL_POLY/FIELD file for which the Special atoms field must be filled because one carbon atom name, CS, will be interpreted as a cesium atom.

  The aim of the Special atoms field is precisely to avoid such problems. The format for the Special atoms field is
  atom name1:element1 sep atom name2:element2 ... where sep can be a white space, a comma or a semicolon.
  In the example showed in figure 4.7, the string CS:C should be entered in the Special atoms field. Interestingly, the Special atoms field can also be used to specify united atoms. The syntax is exactly the same but, in that case, the element name must be replaced by the MMTK united atom code (e.g. CH3, CH2, CH, NH, NH2, NH3, OH, SH ...).

- MMTK NetCDF output file
  Format: string
  Default: None
  Description: the name of the MMTK NetCDF trajectory that will be written.

Next: Discover to MMTK Up: Trajectory conversion Previous: CHARMM/X-PLOR to MMTK Contents