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Using nMOLDYN

by Konrad Hinsen last modified 2011-03-30 19:45

What you need to know to use nMOLDYN.

Trajectories

nMOLDYN expects trajectories to be in netCDF format and follow the conventions of the Molecular Modeling Toolkit (MMTK). Trajectories that have not been produced with MMTK or MMTK-based programs must be converted to MMTK format before they can be analyzed with nMOLDYN. This conversion is necessary because no other common trajectory format permits efficient access both to conformations at a given time and to one-atom trajectories for all times. In addition to providing such an access, the netCDF format has several advantages that make it particularly suitable for archiving trajectories:

  • compact files (binary storage)
  • machine-independent format
  • fully self-contained, all required information about the system is stored in the trajectory file

nMOLDYN comes with two converters for foreign formats:

  • dcd_to_nc converts from the DCD format used by the programs CHARMM, X-PLOR, and NAMD. In addition to the DCD file, a compatible PDB is required as a system definition. Note that DCD files are machine-dependent, the converter accepts only files that are compatible with the machine it runs on.
    There is also an inverse converter, nc_to_dcd.
  • dlpoly_to_nc converts from the DLPOLY format. It reads the DLPOLY files FIELD and HISTORY in order to produce a trajectory file in netCDF format.
Run any of these converters without input arguments in order to get usage instructions.

An elaborate converter for AMBER trajectory files is available separately.

Graphical Interface

The simplest way to use nMOLDYN is via the graphical user interface, which is called xMoldyn. All calculations are accessible via the graphical interface, however, only a standard set of atom selections is provided.

In order to perform the actual computations, xMoldyn starts background jobs using the command-line interface pMoldyn. This means that you can leave the graphical interface once the job is running, the background job will continue.


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