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Update the docs with info about the DRH interaction
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lorenzo-rovigatti committed Oct 9, 2023
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12 changes: 10 additions & 2 deletions docs/source/input.md
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Expand Up @@ -36,7 +36,7 @@ These are the options that control the overall behaviour of the simulation and o
* `time_scale = linear/log_lin`: a linear time_scale will make oxDNA print linearly-spaced configurations. a log_lin will make it print linearly-spaced cycles of logarithmically-spaced configurations.
* `print_conf_interval = <int>`: if the time scale is linear, this is the number of time steps between the outputing of configurations, otherwise this is just the first point of the logarithmic part of the log_lin time scale.
* `print_energy_every = <int>`: number of time steps between the outputing of the energy (and of the other default observables such as acceptance ratios in Monte Carlo simulations).
* `[interaction_type = DNA|DNA2|RNA|RNA2|LJ|...]`: Particle-particle interaction of choice. Check the documentation relative to the specific interaction for more details and the supported interaction-specific options. Defaults to `DNA`.
* `[interaction_type = DNA|DNA2|RNA|RNA2|DRH|LJ|...]`: Particle-particle interaction of choice. Check the documentation relative to the specific interaction for more details and the supported interaction-specific options. Defaults to `DNA`.
* `[max_io = <float>]`: the maximum rate at which the output is printed, in MB/s. This is a useful option to avoid filling up the disk too quickly. Increase the default value (1 MB/s) at your own risk!
* `[fix_diffusion = <bool>]`: if true, particles that leave the simulation box are brought back in via periodic boundary conditions. Defaults to `true`.
* `[fix_diffusion_every = <int>]`: number of time steps every which the diffusion is fixed. Used only if `fix_diffusion = true`, defaults to 100000 ({math}`10^5`).
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* `[salt = <float>]`: the salt concentration in molar (M). Defaults to 1.
* `[mismatch_repulsion = <bool>]`: if `true`, add a repulsion between mismatches. Defaults to `false`.
* `[mismatch_repulsion_strength = <float>]`: set the strength of the repulsion between mismatches. Used only if `mismatch_repulsion = true`, defaults to `1`.
* `[mismatch_repulsion_strength = <float>]`: set the strength of the repulsion between mismatches. Used only if `mismatch_repulsion = true`, defaults to `1`.

## Options for `DRH` simulations

* `[use_average_seq = <bool>]`: use the average-sequence parameters. Defaults to `true`.
* `[seq_dep_file_DNA = <path>]`: path to the location of the file containing the DNA sequence-dependent parameters. Mandatory if `use_average_seq = false`.
* `[seq_dep_file_RNA = <path>]`: path to the location of the file containing the DNA sequence-dependent parameters. Mandatory if `use_average_seq = false`.
* `[seq_dep_file_DRH = <path>]`: path to the location of the file containing the DNA-RNA sequence-dependent parameters. Mandatory if `use_average_seq = false`.


## Options for `LJ` (Lennard-Jones) simulations

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