DOI: 10.5281/zenodo.1753767
title: Initialization files and data supporting https://arxiv.org/abs/1506.09008

description: ###Preamble###

This upload contains initialization files and data for simulations reported in:<br>
https://arxiv.org/abs/1506.09008: Coarse-grained modelling of strong DNA bending II: Cyclization

The initialization files allow a user to repeat the reported simulations using the oxDNA model. oxDNA is available for download from:<br>
https://dna.physics.ox.ac.uk/index.php/Main_Page. <br>
The use and meaning of the input and output files are documented extensively on this wiki. 

<br>
###Organisation### 

A pdf copy of the main text and supplementary material of the relevant paper are provided as main.pdf and SI.pdf in the head directory. Simulations are organised by system type within subdirectories.

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The "Basic cyclization" folder contains the files for sequence-independent simulations of cyclization, for varying duplex and single-stranded overhang lengths. Folder DXXCYY corresponds to simulation of a cyclization system with Nd = XX and Nbp=YY, with the meaning of these symbols given in the paper. These simulations underlie:<br>
- The black data points in Fig. 3, 7 and S4 (alongside data from the simulations in the "Dimerization" folder), <br>
- The data in Fig. 4 and S5.<br>
- The data points connected by solid lines in Fig. 5.<br>
- The black data points in Fig. 6.<br>
- The black data points in Fig S2(a), and the data in Fig. S2(b)<br>
- The black data points in Fig. S3(a)

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The "Dimerization" folder contains the files for the simulations of dimerization, at the two reference concentrations 336nM and 2690nM. For simulations at 336nM, the folder bimolecularXX contains files for the sequence-independent simulation with XX = Nd1+Ns, and bimolecularXX_seq contains the sequence-dependent variants. For simulations at 2690nM, the folder bimolecularXX contains files for the sequence-independent simulation with XX = Nd1+Nd2+Ns, and bimolecularXX_seq contains the sequence-dependent variants. Note that the folders bimolecular73 and bimolecular101_seq were accidentally deleted, and the output data is missing. Input files for bimolecular73 have been recreated (the bimolecular101_seq has not been recreated because these simulations were of very limited importance for the paper). 

These simulations provide:<br>
- The data points in Fig. 3, 7 and S4 (alongside data from the simulations in the "Basic cyclization" folder and the "Perturbations" folder), <br>
- The data points connected by dashed lines in Fig. 5.<br>
- The grey data points in Fig. 6.<br>
- The data in Table S2.

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The "Perturbations" folder contains the files for cyclization simulations that do not correspond to sequence-averaged, defect-free systems.<br>
- Folders DXXCYY_seq and DXXCYY_* contain files relevant to simulations of cyclization with Nd = XX and Nbp=YY, incorporating sequence-dependence. These simulations underlie the brown/blue/mauve data points in Fig. 3, 7 and S2b (alongside data from the simulations in the "Dimerization" folder).<br>
- Folder D5969mm contains files relevant to the simulation of a mismatch containing-sytem, with data reported on Table S3 and Figure S3 (intact simulations can be found in the "Basic cyclization" folder). <br>
- Folders D87C97, D87C97n1, D87C97n2 and D87C97nn contains files relevant to the comparison of a system with no nicks, a nick in position 1, a nick in position 2, and a double nick, respectively. Data are reported in Table S3 and Fig. S3(b).

<br>
###Content###

For each system, a "closed1" and an "open1" folder are present. These correspond to the two windows of umbrella sampling that were performed separately.  Within each folder are the necessary initialization files to run the simulations exactly as reported in the paper, simply by calling oxDNA from within the folder, using "inputVMMC" as the input file. Also included are output files for a single realisation of the simulation. The meaning of these files are outlined at https://dna.physics.ox.ac.uk/index.php/Main_Page. 

Note that the results in the paper were all obtained from 5 independent replicas, using different initial conditions and different seeds. These can be (statistically) recreated simply by drawing random starting configurations from the single available traj_hist file.  

<br>
###A note on topology###

Many of these simulations were performed with "unique" topology, which prevents non-native base pairing. In the topology files, instead of indicating the base type with a letter (A, C, G or T) in the second column, an integer 0 &lt; n or n &gt; 10 is used instead.<br>
- If n modulo 4 =0, the base is treated as possessing the interaction strengths of A but will only bind to a base with a type m = 3-n.<br>
- If n modulo 4 =1, the base is treated as possessing the interaction strengths of C but will only bind to a base with a type m = 3-n.<br>
- If n modulo 4 =2, the base is treated as possessing the interaction strengths of G but will only bind to a base with a type m = 3-n.<br>
- If n modulo 4 =3, the base is treated as possessing the interaction strengths of T but will only bind to a base with a type m = 3-n.

In addition, please note that the topology files for the dimerization simulations at 336nM were set out slightly strangely, in that base IDs are not assigned contiguously to contiguous sequences of bases in a strand at some points. Nonetheless, the connectivity specified by these topology files is correct. <br>