Petr Sulc

Dear Drew, The file format in which the positions are stored is described here: https://dna.physics.ox.ac.uk/index.php/Documentation#Configuration_file You can use our online tool, oxView.org, to interactively calculate distance between selected nucleotides, just by dragging and dropping the file into the browser window. We also offer a python script distance.py here: https://github.com/sulcgroup/oxdna_analysis_tools that carries out the calculation for you, without having to manually deal with periodic...

Dear Pranav, The scripts in UTILS directory are legacy software and are no longer updated or supported. You can use e.g. the python library available here: https://github.com/sulcgroup/oxdna_analysis_tools as for the visualization of simulation files, we recommend either using oxView.org (runs inside web browser) or install cogli2 software: https://sourceforge.net/projects/cogli1/

Please note that if you want to use the GPU version of the code, you need to build it iwth cmake -DCUDA=1 and have a NVIDIA gpu on the computer where you run it. If you do not have a GPU, you will need to run the MD version of the code (which is ok for structures up to few hundred nucleotides). Otherwise I recommend oxDNA.org server. It provides free GPUs for simulation and also automatically generates and executes the relaxation input file that helps to aleviate some of the issues with the stretched...

I recommend using the "Relax structure" option on oxDNA.org. If you want to run it locally, it consists of using max_backbone_force = 5 which can help relaxing stretched backbone bonds, a common occurrence when importing from caDNAno and other design tools. I then recommend running the simulation for at least 10^6 or more MD steps with this parameter. If the structure is larger than few hundreds nucleotides, GPU is recommended.

Dear Derek, You interpretation of columns is correct. I just add that DH stands for Debye-Huckel (approximation of electrostatic repulsion between backbone) interaction, and BEXS is the excluded volume interaction between nearest neighbors on the same strand, and NEXC is the excluded volume between nucleotides that are not nearest neighbors. -1 unit of energy corresponds to 41.42 pN nm, which is about 10 kT for T = 298K

We have faced similar issue before, and what we found works best is to do the edits in oxView tool. We have a scripting interface that allows you programatically edit the imported structure (we are working on documenting it right now). You can just import the original design, without the extensions, open a javascript console while in OxView, and run this code: function extend_overhang(strand = systems[0].strands[0],){ // we are interested in 5ps? const p5 = strand.end5; // fetch 5' orientation const...

if you are on linux system, then export PATH=$PATH:path_to_directory_where_binary_is_installed Please note that on this forum, we can only provide support directly related to using the code and simulations. We assume that the user has a functioning command line environment with functioning cmake and gcc compiler. Other places, like stackoverflow, can be used for general questions about using command line or having issues with other software installation

That looks like cmake is not installed on your system properly. Maybe you did not correctly setup the path to the cmake binary?