MBG wiki: Editing revision 17 of Quick view of large trajectory (DCD) files

Editing old revision 17. Saving this page will replace the latest revision with this text.

<b>/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 :

<code>
carma my.dcd my.psf
</code>

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

You should see something like

[[image: carma version 0.8]]

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/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.

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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):

<code>
carma -v -gl 70.0 -atmid "ALLID" protein_only.dcd protein_only.psf
</code>

[[image: carma viewer image A]]

<code>
carma -v -gl 70.0 -atmid "ALLID" -segid " A   " -segid " B   " protein_only.dcd protein_only.psf
</code>

[[image: carma viewer image B]]

<code>
carma -v -gl 70.0 -segid " A   " -segid " B   " protein_only.dcd protein_only.psf
</code>

[[image: carma viewer image B2]]

<code>
carma -v -gl 120.0 -atmid "ALLID" -segid " A   " -segid " B   " protein_only.dcd protein_only.psf
</code>

[[image: carma viewer image C]]

<code>
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
</code>

[[image: carma viewer image D]]

<code>
carma -v -gl 90.0 -atmid " SOD " -atmid " CLA " -atmid " OH2 " all_atoms.dcd all_atoms.psf
</code>

[[image: carma viewer image E]]

<code>
carma -v -gl 90.0 -atmid "ALLID" all_atoms.dcd all_atoms.psf
</code>

[[image: carma viewer image F]]

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