Is it possible to capture all the collision and fragmentation processes as XYZ files? #28
Replies: 2 comments 2 replies
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Hi Tobias, I'm not quite sure what you are asking for. As you can see in your example, the fragmentation occurs in the mean-free-path MD, after the second collision and before the third collision. In this case, the energy transfer from collision-to-internal energy takes some time to be distributed into the vibrational frequencies, so that the second collision is enough to induce the fragmentation, but just "needs" more time. This mean-free-path (MFP) is obviously shorter than in the experiment, but can be a huge factor in computational time. In these MDs, no collision gas atom is sampled, because 1) the ion-gas distance is very large, i.e. no influence of the gas atom, 2) the xyz files would explode in size and 3) would also affect the visualization of the MD. I'm not quite sure what you mean with "hidden" files. The MFP MD, which is written in the MDtrj.1.2.2 file, is in the same format as the EI MD trajectory, so these are .xyz files and should easily be opened with all visualization programs. I agree that naming the CID steps .xyz while not doing the same for the MDs is not very consequential, but was planned to better discriminate between xyz files of the fragments (e.g. 3.1.2.xyz) and the MDs (either CID MD or MFP MD). From my logic, it would make more sense to rename the CID.xyz files to only CID to better discriminate. What do you think? All fragments and ions (even if not fragmented) are always written out after each collision, as well as each MFP MD. So all processes are captured and you can see where exactly fragmentation occurs. In your case, the ion gains enough energy to dissociate in the second step, but not in a direct fragmentation (the exact moment of the collision leads to fragmentation), but rather in a statistical fragmentation (internal energy conversion). These statistical fragmentation are better in capturing rearrangement reactions, so having a collision as well as a MFP MD is only beneficial for the simulation. |
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@JayTheDog Thanks. So I would not rename the CID files, also the numbering is OK, its just hard to understand and decipher for novice users that have never worked with QCxMS. All your explanations sound logical to me. Basically I am concerned with (1) ease of use for new users and (2) provenance that can be easily followed.
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I'm confused, why do you ping me in this thread? |
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Sorry that was for @JayTheDog |
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Hi,
I was running a CID simulation of scopolamine, but not all the collision steps are actually captured. In the two major steps no fragmentation occurs, captured as trajectory files for Avogadro or Jmol (CID1.xzy and CID2.xyz). In the third CID3.xyz file the fragmentation starts immediately with a smaller fragment, but one can not actually visualize the collision, its only captured in the MD files which are (hidden) xyz files, without the collision gas. So if the dissociation occurs after CID2, then it would be nice to automatically rename the "MDtrj.1.2.2" file also into XYZ. Also the specific filenames could directly added to the qcxms.out file to easier find associated reactions. The naming schema gives it away, but its not always easy to decipher the order of those files.
From a mass spectrometric perspective I think the visualization of all CID fragmentation processes is very important, especially those where the molecules collide, where the bond breaks, which additional rearrangements occur. So I was wondering if this could be enabled as a future feature, I added it here as an idea in discussions, in order to avoid spamming the issue board. I added the visual example and the trajectory files here scopolamine-minibench.tar.gz.
Tobias
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