Hi everyone,
I am typing some answers right into text of my previously stated questions about NMR simulator.
My thanks goes to Pavel Kessler, Michael Engelhard and Amy Freund for providing me with helpful feedback.
Another generic comment I'd like to pass on regarding NMR simulator is as follows. If you are considering acquiring the teaching licenses that contain NMR simulator beware that these clash with any existing processing licenses (that don't come with NMR simulator). Two servers would need to be set up. I ran into this issue and in the end I still don't know how I would set up two servers. Instead, the problem was solved by forgoing the teaching licenses and exchanging them with NMR simulator-only licenses, where we just simply had to add the license code text to the license.dat file for our existing processing licenses.
All the best,
Markus
Dear Bruker Users,
For teaching purposes, I have been in the process of learning how to use NMR simulator. (We use Topspin 1.3.) I ran into two main issues I have not been able to resolve on my own. Any hints to point me in the right direction are most welcome.
1.) I am unable to successfully simulate a selective presaturation experiment. I did make sure that the simulation is set to full relaxation, the spin system has values for T1 and the offset is properly set. I suspect it has to do with setting the powerlevels. NMR simulator uses absolute values in Hz units and I just have no good handle in assessing what values are appropriate, even after reading the little bit of info available in the NMR simulator manual on page 108. I tried by trial and error a number of settings but to no avail.
The current NMR-Sim version does not simulate relaxation
during rf pulses ( see Chapter 2.2 Relaxation) and so you cannot
correctly simulate sequences using a long cw pulse for presaturation.
2.) I was successful in simulating a T1 experiment. It would be nice to have students use the same relaxation analysis in Topsin 1.3 to confirm the known T1 value. However, the delay list information does not transfer over from NMR simulator to the obtained data set visible in Topspin, and the relaxation analysis module does not work. I re-created the delay list, but this still does not seem to get recognized by the relaxation analysis routine.
This problem will be fixed in next patch level. As for now there are two options around it by modifying the data files outside of Topspin. I was able to work out option 2:
Option 1:
you need to make a physical copy of the used vdlist to the EXPNO directory. There's no need to manipulate the acqu(s) files, it's enough to just copy the file vdlist under that same name to the EXPNO directory.
Option 2:
Once the data is generated by NMRSim, and transferred to Topspin, you will need to
(a) manually add the delay list to the experiment's directory, not the general Topspin directory for vdlists. Go to <Topspin home>/data/<user name>/nmr/<experiment name>/<EXPNO> and edit the acqu and acqu files with the name of the delay list. You can easily edit the acqu directory within Topspin instead of editing the text of the file, but the status file, acqus will need to be edited outside of Topspin.
(b) add the actual delay list file to the same directory listed above. Be sure there is no .txt or other extension in the file name.
Markus Hoffmann
Department of Chemistry
SUNY Brockport
Phone: (585) 395-5587
FAX: (585) 395-5805
mhoffman@brockport.edu
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