[DOCUMENTATION] What is a trajectory file and energy file? How should I understand the output files?

[songge1111]

What is the documentation missing?

I am new to molecular simulation for nucleic acids, and I don't understand the trajectory file and the energy file.

1. What does a trajectory file mean? What does an energy file mean?
2. The trajectory file is required when I run a new simulation. So How should I get the trajectory file of my interested RNA sequences? Or do I just need to leave it blank with a file name trajectory.dat ?
3. The energy file is required when I run a new simulation. So How should I get the energy file of my interested RNA sequences? Or do I just need to leave it blank with a file name energy.dat ?
4. I simulated a single-strand RNA with a length of 21nt. Firstly I got the .top and .dat files from the utils/generate-sa.py script with my interested RNA sequence. Because the trajectory.dat and energy.dat are required and I don't know how to generate these files, I left them blank and started to run the task. At the end of the run, I got output.dat, log.dat, and last_conf.dat, the energy.dat was not blank anymore, but the trajectory.dat was still empty. So How should I explain these output files? (I attach my input and output files here: test_oxDNA_tast-2024-12-09.zip)

Can you provide some documents, links, or videos that teach a new one to start and understand his/her oxDNA inputs and outputs? Thanks a lot! :)

[lorenzo-rovigatti]

The energy and trajectory files are written as the simulation proceeds, you don't need to create them beforehand. The frequency with which the files are updated depend on the options specified in the input file. You can have a look at the available options here.
As per their meaning, these are pretty standard files as MD packages go. The energy file contains the MD time and the potential, kinetic and total energy per nucleotide, while the trajectory contains sampled configurations. The configuration format can be found here.