Activity for Jonathan Doye
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Jonathan Doye posted a comment on discussion General Discussion
I think the problem is that your script does not take into account the periodic boundary conditions whereas oxView does. Your configuration seems to have sets of nucleotides in 5 periodic images of the cell.
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See here for a description of the RepulsionPlane: https://dna.physics.ox.ac.uk/index.php/Documentation#Repulsion_plane . In this case the repulsion is harmonic.
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Yes, the code does have the facility to include a flat surface, but not in a material-specific way. See here for details of a wall with a Lennard-Jones type interaction: https://sourceforge.net/p/oxdna/discussion/general/thread/f4e7065732/
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Okay, I understand the problem. As the extensions in the cadnano file are on unoccupied parts of virtual helices that are in the plane of the origami, the initial long bond connecting the extension to its attachment point will pass through other parts of the origami. In that case whether after relaxation the extension ends up on the correct side or not entangled with other parts of the origami will be somewhat down to luck. To resolve the problem, I'd redraw the extensions in the cadnano file so...
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I think I roughly understand what you are trying to do, but if you could show some pictures of your starting and end configurations, it will be easier to diagnose the problem. "Unnatural" initial configurations aren't necessarily a problem as long as there is a clear path for the different sections to relax to a more physically sensible geometry. However, if parts have to pass through each other this will likely be prevented by the oxDNA excluded-volume interactions. Those tails which end up on the...
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If you output the position(s) of the nucleotide(s) that are subject to the trap, then if you know the position of the trap, you can calculate the force exerted by the trap using Hooke's Law. The magnitude of the fluctuations in the instantaneous trap forces can be quite significant and will scale roughly as the square root of the force constant. For example, in some of the force-extension plots in http://dx.doi.org/10.1021/acsnano.8b01844 both the instantaneous force and a running average are plotted;...
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Dear Tan, The free energy is not something that can be associated with a single instantaneous configuration, unlike say the potential energy, and so is not simply outputted by the program. If one wants to calculate the difference in free energy F between two states A and B, it is related to their relative probabilities as follows: Delta F = F_B-F_A = -k_B T log (p_B/p_A) So, if in a simulation the equilibrium between the two states is well sampled, one can simply use the above. If, however, there...
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I think for DNA systems, it is always better to consider the free energy associated with a process rather than just the energy. But, yes it is possible to compute the free energy of bending (see here for bending a duplex: http://arxiv.org/abs/1506.09005 ), but computing such free energies, of course, is not as straightforward as computing energies. Also, when you talk about "the bending energy of a 3D structure" you should think about what you mean, e.g. what is the unbent reference structure to...
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I think for DNA systems, it is always better to consider the free energy associated with a process rather than just the energy. But, yes it is possible to compute the free energy of bending (see here for bending a duplex: http://arxiv.org/abs/1506.09005 ), but computing such free energies, of course, is not as straightforward as computing energies. Also, when you talk about "the bending energy of a 3D structure" you should think about what you mean, e.g. what is the unbent referenence structure to...
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This error refers to the distance between the backbone sites (not the centre of mass sites) of bonded neighbours being larger than the maximum allowed by the backbone FENE potential. The programme calculates the positions of these sites from the centres of mass of their nucleotides and their orientations. This error is usually a result of incomplete relaxation of the initial structure (nb. it can also be due to accidentally switching between oxDNA1 and oxDNA2 as the positions of the backbone sites...
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There are two ways this can be done. 1) Harmonic traps acting between nucleotides in the overhangs that should be base-paired can be added. (https://dna.physics.ox.ac.uk/index.php/Documentation#Harmonic_trap) These will bring the nucleotides close enough together that they should base pair. Once base-paired these traps can then be removed. (If the nucleotides are intially quite distant, it can be useful to change the equilibrium separation of the harmonic trap as a function of time to more gently...
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