[MMTK] self-contained trajectory file

Eric Pettersen pett at cgl.ucsf.edu
Fri Sep 12 23:36:24 UTC 2014

Hi all,
	I feel like I must be missing something simple or obvious.  Some people have been trying to extend UCSF Chimera to compute and write trajectories using MMTK.  The issue is that Chimera subclasses Molecule in order to transfer its molecular data into something MMTK can use to run the MD computation.  When MMTK writes the trajectory it puts the info for restoring the Molecule in the trajectory file, but it can't really read/restore from that file because it expects an entry in the Molecule database (e.g. "#0" or "1yti") that does not exist.  Is it possible to write a trajectory file for arbitrary chemical systems that don't depend on custom database entries (i.e. all the necessary information is in the trajectory file itself)?
	I tried using MoleculeFactory instead of subclassing Molecule, but that also writes Molecules into the trajectory file to the same result.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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