TUTORIAL B6 - SECTION 7
Using Sirius with AMBER
By Sasha Buzko
7) Buffered trajectory loading and saving individual frames
Sometimes simulations cover long spans of time with several thousand frames in each run, which dramatically increases size of the data files. Another possibility is simulations of very large systems with atom counts of over several thousand. Since desktop computer systems cannot accommodate arbitrarily large data sets in main memory, Sirius provides a mechanism for loading such files in a buffered manner. In this case, only a small portion of the entire data set is loaded - typically, the beginning 50 frames and 50 frames immediately after the current frame. When the trajectory is played back, the necessary frames are dynamically loaded from the files on the hard drive. This provides a considerable savings in memory and permits visualization of data sets of virtually any size. One drawback of the buffered loading is that free fast-forwarding along the trajectory and jumping backwards are restricted due to file reading complexities. Otherwise, the display is as interactive as that using non-buffered loading.
To enable buffered loading, go to Data menu of the MD panel and select Use frame buffering. With this setting any multifile datasets will be loaded using buffering. If you attempt to load a single coordinate file that is over 20 MBytes, Sirius will prompt you for a decision on whether to use buffering for that specific file.
With buffering enabled, let's load files that we have used before: step1.out.gz and step2.out.gz. For these files to work properly, you will need TC5b.prmtop, step1.mdcrd.gz and step2.mdcrd.gz to be present in the same directory. Load the two out files. Note that Frame count in the MD panel has stopped at 50 and that the number is enclosed in parentheses. This means that 50 frames have been loaded so far, and parentheses indicate that the entire trajectory hasn't been passed yet. Once you start playback, loading will resume to keep the number of buffered frames approximately 50 frames ahead of the current position.
Until the entire trajectory has been passed at least once (at which point frame count loses parentheses and displays the total count), you can't drag the slider to arbitrary positions within the trajectory. Also, stepping backward is disabled in the buffered mode. All other functions are the same as before. Even though the restrictions are relatively minor, we recommend using buffered loading only in the cases where direct loading will put too much strain on the system resources.
Frequently, it is desirable to be able to save a frame of a simulation to a separate file. In Sirius, this is accomplished very easily using standard facilities of the environment. You can try this feature using the loaded structure. It doesn't matter whether it's being loaded directly or using buffering. Simply stop playback at the desired frame, select Save structure... from the File menu of the main window, enter the desired name (extension is optional), and choose file format from the pulldown menu. You can save structures in PDB, MOL2 (Tripos) or SDF (MOL) fie formats.
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