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lorenzo-rovigatti / oxDNA

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings
https://dna.physics.ox.ac.uk/
GNU General Public License v3.0
38 stars 26 forks source link

[BUG] Truncated trajectory #67

Closed Boyu-Liu03 closed 9 months ago

Boyu-Liu03 commented 9 months ago

Describe the bug Sometimes OxDNA (web-browser version) produces a trajectory file that is truncated to 10 configurations of 10k steps to a total of 100k steps, with different input total_steps and print_config steps.

To Reproduce Steps to reproduce the behavior:

  1. I ran simulations
  2. Here are the input files: V3.1_51_NC_T_R.log V3.1_51.NC.T.R traj log.pdf

However, I have also seen this issue with different input files under the same simulation parameter file: V3.1_51_NC_T_R_input.txt But also different input files with different simulation parameter files.

Expected behavior

I expect the simulation to run and come back successful, but when downloading the trajectory, notice the incredibly small size of usually around 14mb compared to around 300mb that I usually get for other simulations using the same simulation parameters. Then, I expect that on the total jobs list, that the final configuration is greyed out and unavailable dispite the simulations ran successfully.

Desktop (please complete the following information):

Additional context Add any other context about the problem here. I have also emailed the oxdnahelp email account about this issue with specific job identification numbers too.

lorenzo-rovigatti commented 9 months ago

If you look at the last part of the log file you can see that the simulation crashes with an "out-of-memory" error. The box size you are using is most likely too big,

ErikPoppleton commented 9 months ago

To follow up, the 10 configurations you're seeing are from the 10k Monte-Carlo steps that the relaxation protocol on the webserver begins with to remove excluded volume problems. If you have specific problems with the webserver version, you should send an email to the address listed in the FAQ page, they can help more with webserver-specific problems.

Boyu-Liu03 commented 9 months ago

Oh okay so sorry about the confusion then. Thank you all so much for the quick response!

Boyu-Liu03 commented 9 months ago

I will be using the email address moving forward!