Execution error in rocket-export_oxDNA.oxdna/top on oxdna.org

[dfajita]

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:

Error

INFO: seeding the RNG with 1259777439 
INFO: Initializing backend 
INFO: Backend precision: double 
INFO: Simulation type: MD 
INFO: The generator will try to take into account bonded interactions by choosing distances between bonded neighbours no larger than 2.000000 
INFO: Using '' as the input for sequence-dependent values 
INFO: Running Debye-Huckel at salt concentration = 1 
INFO: Using different widths for major and minor grooves 
INFO: pid: 13345 
DEBUG: Debye-Huckel parameters: Q=0.054300, lambda_0=0.361646, lambda=0.357493, r_high=1.072479, cutoff=2.571515 
DEBUG: Debye-Huckel parameters: debye_huckel_RC=1.608718e+00, debye_huckel_B=8.766182e-03 INFO: The Debye length at this temperature and salt concentration is 0.357493 
ERROR: Distance between bonded neighbors 15 and 16 exceeds acceptable values (d = 1.830765)

I assumed that I needed Relaxation, therefore I checked the Needs Relaxation box. But the outcomes were similar.

Error

INFO: seeding the RNG with -1692663956 
INFO: Initializing backend 
INFO: Backend precision: double 
INFO: Simulation type: MC 
INFO: Using unphysical backbone (DNA_relax interaction) 
INFO: The generator will try to take into account bonded interactions by choosing distances between bonded neighbours no larger than 2.000000 
INFO: Using '' as the input for sequence-dependent values 
INFO: Using default strength constant = 32.000000 for the DNA_relax interaction 
INFO: pid: 13451 
INFO: Using a maximum backbone force of 10 (the corresponding mbf_xmax is 0.169258) and a far value of 0.04

I would appreciate it if you could inform me of the required preprocessing to run ENSnano exported files in oxDNA. Thanks.

[thenlevy]

Hello, Before running a simulation on oxdna.org, the file needs to be prepared on oxview.org

See procedure 3 and 4 here https://www.nature.com/articles/s41596-022-00688-5.epdf?sharing_token=Mz9sVsJlpDz_BABfhLgql9RgN0jAjWel9jnR3ZoTv0O6C-DLCrV6DPpJ2twUUdRjhuov0G9ve-OWL_YTnU4N8KRzIYndLudMsrqQqpaPKsW8XYioSMWe5DAjKC5x_I7gsTCyopRaCMY3UoE9Hsr1VwvJ7tAO0tNWTFClHTtldPg%3D

My understanding is that oxview performs a pre-relaxation that makes the input more suitable to oxdna.org

[dfajita]

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!