Open dfajita opened 1 year ago
Hello, Before running a simulation on oxdna.org, the file needs to be prepared on oxview.org
My understanding is that oxview performs a pre-relaxation that makes the input more suitable to oxdna.org
Thank you for being so helpful!
I misunderstood that the calculations could be performed from the oxDNA export file right away. I now understood that this is an issue with how to use OxView rather than an ENSnano one. Sorry!
I have verified that the relaxation calculation using "Simulation type: MC" can be done on oxView as you recommended. I appreciate your thoughtful advice very much.
To be honest, I still have the issue of staples breaking after relaxing in the MD simulation, however I think the issue is with OxView parameter setting. I'll exert a little more effort.
Thanks again for your kind support!
Thank you again for your exceptional software development.
I am a beginner in both ENSnano and oxDNA. So, I first attempted to run a simulation on oxen.org using the files in ENSnano-rocket_design.zip, which can be downloaded from http://www.ens-lyon.fr/ensnano/#rocket.
I uploaded two files (rocket-export oxDNA.oxdna and rocket-export oxDNA.top) and executed a "submit job" with the default settings.
I did, however, get the following error:
I assumed that I needed Relaxation, therefore I checked the Needs Relaxation box. But the outcomes were similar.
I would appreciate it if you could inform me of the required preprocessing to run ENSnano exported files in oxDNA. Thanks.