MBG wiki: Quick view of large trajectory (DCD) files

Carma is evolving really fast these days. The rest of this page is history (and as such, is being kept). As of v.0.8 of carma, you can view a trajectory file quickly by saying :

carma my.dcd my.psf

That's all. Just hit enter to start from the beginning, or select starting frame.

You should see something like

Carma is evolving quickly these days. For all examples that follow please add a '-trace' flag to tell carma to draw a backbone trace. There are more new features in carma, like stereo viewing, swinging the molecule around, etc. Have a look in carma's manual page.

The most powerful program for viewing trajectory files is vmd. The problem is that vmd attempts to load the whole trajectory file in memory. With the limited physical memory resources available on our nodes (256 MBytes for newer nodes) if you try to run vmd with a dcd larger than 512 MBytes the following will happen :

As vmd reads data from the disk (and onto physical memory), the various processes' data will be moved (by the kernel) to swap. The result will be momentary 'freezes' of X and the other programs running (including unix shells).
As vmd starts using swap both for itself and for the DCD, you will experience longer 'freezes'.
Finally, when the 512 MBytes mark is hit, kernel will enter what is known as out-of-memory condition, and will kill vmd. Few seconds later you should be back to business (with a responsive system), but without vmd.

A quick way to view large DCD files without large memory consumption has been implemented in carma. But : the viewer is primitive, extremely primitive. You can only view things along the three orthogonal axes (x, y, and z), the only representation available is simple dots, and the choice of colours is obscure. Typical. Still, this is how is goes (use the xyz keys to change views):

carma -v -gl 70.0 -atmid "ALLID" protein_only.dcd protein_only.psf

carma -v -gl 70.0 -atmid "ALLID" -segid " A   " -segid " B   " protein_only.dcd protein_only.psf

carma -v -gl 70.0 -segid " A   " -segid " B   " protein_only.dcd protein_only.psf

carma -v -gl 120.0 -atmid "ALLID" -segid " A   " -segid " B   " protein_only.dcd protein_only.psf

carma -v -gl 90.0 -atmid "ALLID" -segid " A   " -segid " B   " -segid " WT1 " -segid " C   " -segid " D   " -segid " SOD " all_atoms.dcd all_atoms.psf

carma -v -gl 90.0 -atmid " SOD " -atmid " CLA " -atmid " OH2 " all_atoms.dcd all_atoms.psf

carma -v -gl 90.0 -atmid "ALLID" all_atoms.dcd all_atoms.psf