Plotting Mass Spectra (PlotMS)

The PlotMS utility is provided in order to visualize your results. The newest version can be found in the PlotMS repository. The program analyzes the qcxms.res or qcxms_cid.res file and combines the results using the ~/.mass_raw.agr template file to create the mass.agr and the results.jdx files in your working directory.

This may be useful to check for convergence in case you are running more trajectories than actually needed for good statistics. You can plot your spectra as soon as the production run has started.

  1. Change into your working directory and run plotms. This should generate the mass.agr file.

  2. With the mass.agr file, visualize your QCxMS spectrum with:

xmgrace mass.agr
  1. For a comparision of EI spectra, the experimental spectrum can be downloaded from the NIST database if available (JCAMP-DX format). Copy it to the working directory as exp.dat. PlotMS reads the exp.dat and compares your calculated spectrum directly to the experiment (inverted). There is currently no feature to do this for the CID spectrum as well.

Visualization of Trajectories

There are some useful commandline options to manipulate your results.


print spectra “mass % intensity counts Int. exptl” to stdout with “Int. exptl” (experimental) taken from exp.dat but not all exp peaks are exported, if no theoretical counterpart exists

-f <filename> or -f <name_of_res_file>

provide .res file for plotting the spectrum

-t <x> <y>

couting ions with charge x to y (give the value, e.g. “-t 1 2” for charge 1 to 2)

-w <real>

broadening the charges by an standard distribution (given in decimal numbers between 0 and 1)

-s <integer>

account only for only secondary and tertiary fragmentations (give the value, e.g. “-s 2” for secondary)

-m <integer>

set minimum threshold for m/z. Will be calculate the base peak for higher values than


do not calculate the isotope pattern

Visualization of Trajectories

Trajectories are saved in the TMPQCXMS/TMP.XXX directories, where NUM is the first number of the specific trajectory track to be visualized. There are two programs that can easily display the trajectories, which are saved in the files. One is (g)molden, the other is VMD. Obtaining a video (.avi) of a given trajectory is possibly most easily done by loading the trajectory of choice into VMD (file type .xyz).

The msmovie and movie.tcl scripts for VMD generate a visualization using the dynamic bonds graphical representations setting. This allows for movie generation employing the VMD movie maker plug-in. Simply type msmovie X Y in the working directory to load the trajectory TMPQCEIMS/TMP.X/trj.X.Y. For instance, msmovie 1 1 loads the first trajectory of the first folder. Some adjustments according to personal preferences for movie-making may have to be made in these scripts.