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