Hi
I am trying to simulate a tRNA structure (using oxRNA). The simulation does not run and complains about the following in the log file :
ERROR: Distance between bonded neighbors 0 and 1 exceeds acceptable values (d = 1.022702)
What I do not understand is what 'd' represents?
None of the following distances between the two particles 0 and 1 add up to d=1.022702.
(i) Distance between the centers
(ii) Distance between the base sites (center + 0.4 axisvector)
(iii) Distance between the backbone sites ( center - 0.4 axisvector)
Out of which I would expect the third one to be the more appropriate one for bond calculation purposes.
The distance between the backbone sites for these two particles is ~0.71 (well within the 0.5 to 1.0 distance for valid FENE bonds in this case)
Please let me know what I am missing and how I can go about solving the problem.
I am not sure how attachments work on this forum but I am willing to share the topology, configuration and input file if needed.
Thanks
Regards
Sweta
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Hi Sweta,
Yes, the distance reported in your error message is indeed betweeen the backbone sites.
Does the program run at least one step or it stops immediately? If you are using the RNA model, you should include
interaction_type=RNA
in the input file. In case the initial configuration has too large distances between backbone sites, you can instead use
interaction_type=RNA_relax
in the input file, run for ~ 10^5 VMMC iterations and then use the lastconf.dat file as the initial file for regular RNA interaction. If this still does not work, send us your conf, topology and input files (using the attach files link at the bottom of the page in this forum).
Best,
Petr
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi
I am trying to simulate a tRNA structure (using oxRNA). The simulation does not run and complains about the following in the log file :
ERROR: Distance between bonded neighbors 0 and 1 exceeds acceptable values (d = 1.022702)
What I do not understand is what 'd' represents?
None of the following distances between the two particles 0 and 1 add up to d=1.022702.
(i) Distance between the centers
(ii) Distance between the base sites (center + 0.4 axisvector)
(iii) Distance between the backbone sites ( center - 0.4 axisvector)
Out of which I would expect the third one to be the more appropriate one for bond calculation purposes.
The distance between the backbone sites for these two particles is ~0.71 (well within the 0.5 to 1.0 distance for valid FENE bonds in this case)
Please let me know what I am missing and how I can go about solving the problem.
I am not sure how attachments work on this forum but I am willing to share the topology, configuration and input file if needed.
Thanks
Regards
Sweta
Hi Sweta,
Yes, the distance reported in your error message is indeed betweeen the backbone sites.
Does the program run at least one step or it stops immediately? If you are using the RNA model, you should include
in the input file. In case the initial configuration has too large distances between backbone sites, you can instead use
in the input file, run for ~ 10^5 VMMC iterations and then use the lastconf.dat file as the initial file for regular RNA interaction. If this still does not work, send us your conf, topology and input files (using the attach files link at the bottom of the page in this forum).
Best,
Petr