-
Notifications
You must be signed in to change notification settings - Fork 27
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
[Standard Relaxation Procedure] Clarification Needed #112
Comments
Hi! I can't remember on top of my head what oxdna.org does, but maybe @zoombya or @ErikPoppleton do.
Most of the times you'll need some sort of supervision (or to check some heuristics that let your code evaluate whether more relaxation is required). |
The relaxation protocol on oxdna.org uses the files from oxDNA/analysis/example_input_files (actually I think it runs the simulations a bit longer than those files for consistency). We have found that this procedure works for almost all structures. Depending on how good your initial configuration is, you might need to adjust the length of MD relax step or modify the The procedure was first described in section 3.2 of this protocol. We discuss it further in section 4 of this protocol. |
Erik's answer is extremely comprehensive, additionally I wanted to add that it makes little sense to use |
Dear Team,
I am new to using oxDNA and am seeking assistance with the standard relaxation procedure.
I am constructing a pipeline for running oxDNA simulations with a given DNA sequence. The workflow is as follows:
I have used the script below to run the oxDNA simulation.
However, I am encountering issues with the relaxation step. Specifically, I am looking for the equivalent of ticking the relaxation box available on the oxDNA website (https://oxdna.org/).
From my understanding, it might be possible to adjust the simulation parameters for relaxation in the configuration file as described in the oxDNA documentation on relaxation. My question is: can I achieve relaxation by running two consecutive light simulations with modified parameters?
Any guidance or example configurations/scripts for properly implementing the relaxation procedure would be greatly appreciated.
The text was updated successfully, but these errors were encountered: