Author Topic: Visualization of trajectory in Molecular dynamics  (Read 537 times)


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Visualization of trajectory in Molecular dynamics
« on: November 27, 2022, 12:51:43 AM »
Dear Turbomole Experts,

I have been using the line

"t2x >"

after any geometry optimization run (no matter if converged, not converged or job-crashed somewhere) and I got full trajectory in that file, so by


I could view it. Inside there have been lines 66,title,66 lines with xyz data, then 66, title, etc. (I have 66 atoms in my system). The point is, it does not work for my jobex -md run, sadly :-(

After writing this in directory, where jobex -md have been run, my is empty file. I have tried also tm2molden, but molden molden.input let to "no coordinates found" (unlike for geometry optimizations with jobex -relax, where it simply works as expected, at least in cases optimization does not crash).

Honestly, I don't even have idea, where t2x gets the input data to produce (in case of optimization run). If I knew that (my suspection was the "gradient" file, where coordinates and gradient are stored for every cycle... but t2x gradient > in optimization directory does produces an empty file!), I could somewhat find or create file (let us call it from jobex -md run so "t2x" could get trajectory readable by molden...

The best candidate for is mdlog.1, but t2x produces empty output.
I tried to delete all other info from copy of mdlog.1 (mdlog.1.c) than coordinates, place $coord and $end before and after each "snapshot"'s coordinates and run t2x on it and it only transformed the first point.

What shall I do? How do I get file which will molen see as a whole trajectory, please?

Best regards,


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Re: Visualization of trajectory in Molecular dynamics
« Reply #1 on: January 13, 2023, 11:19:55 AM »

in an MD run, the trajectories are stored in the mdlog files.
The log2x tool can be used to create an xyz movie. 

Also, log2egy can be very handy analyse your results.