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Update documentation
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2 changes: 1 addition & 1 deletion _sources/configurations.md.txt
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Expand Up @@ -117,7 +117,7 @@ CGCAAC type=DNA
```

```{note}
Setting `type` only affects the force field when using the DNA/RNA hybrid model (`interaction_type=DRH`). For normal DNA or RNA, the interactions will be determined by the `interaction_type=DNA|DNA2|RNA|RNA2|DRH|LJ...` parameter in the [input file](input.md)
Setting `type` only affects the force field when using the DNA/RNA hybrid model (`interaction_type=NA`). For normal DNA or RNA, the interactions will be determined by the `interaction_type=DNA|DNA2|RNA|RNA2|NA|LJ...` parameter in the [input file](input.md)
```

```{note}
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3 changes: 2 additions & 1 deletion _sources/input.md.txt
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Expand Up @@ -71,7 +71,7 @@ These options control the behaviour of MD simulations.

* `sim_type = MD|FFS_MD`: run either an MD or an FFS simulation.
* `backend = CPU|CUDA`: MD simulations can be run either on single CPU cores or on single CUDA-enabled GPUs.
* `backend_precision = <any>`: by default CPU simulations are run with `double` precision, CUDA with `mixed` precision (see [here](https://doi.org/10.1002/jcc.23763) for details). The CUDA backend also supports single precision (`backend_precision = float`), but we do not recommend to use it. Optionally, [by using CMake switches](install.md#CMake-options) it is possible to run CPU simulations in single precision or CUDA simulations in double precision.
* `backend_precision = <any>`: by default CPU simulations are run with `double` precision, CUDA with `mixed` precision (see [here](https://doi.org/10.1002/jcc.23763) for details). The CUDA backend also supports single precision (`backend_precision = float`), but we do not recommend to use it. Optionally, [by using CMake switches](install.md#cmake-options) it is possible to run CPU simulations in single precision or CUDA simulations in double precision.
* `dt`: the simulation time step. The higher this value, the longer time a simulation of a given number of time steps will correspond to. However, a value that is too large will result in numerical instabilities. Typical values range between 0.001 and 0.005.
* `refresh_vel = <bool>`: if `true` the velocities of the particles in the initial configuration will be randomly sampled from a Boltzmann distribution corresponding to `T`. If `false`, the velocities in the `conf_file` will be used (or an error will be thrown if the `conf_file` doesn't include initialized velocities).
* `[reset_initial_com_momentum = <bool>]`: if `true` the momentum of the centre of mass of the initial configuration will be set to 0. Defaults to `false` to enforce the reproducibility of the trajectory.
Expand Down Expand Up @@ -152,6 +152,7 @@ The following options control the behaviour of MC simulations.
## Common options for `DNA2` and `RNA2` simulations

* `[dh_lambda = <float>]`: the value that lambda, which is a function of temperature (T) and salt concentration (I), should take when T = 300K and I = 1M. Defaults to the value from Debye-Huckel theory, 0.3616455.
* `[debye_huckel_rhigh]`: the distance at which the smoothing of the Debye-Hucker repulsion begins. Defaults to three times the Debye screening length.
* `[dh_strength = <float>]`: the value that scales the overall strength of the Debye-Huckel interaction. Defaults to 0.0543.
* `[dh_half_charged_ends = <bool>]`: if `false`, nucleotides at the end of a strand carry a full charge, if `true` their charge is halved. Defaults to `true`.

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2 changes: 1 addition & 1 deletion _sources/install.md.txt
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Expand Up @@ -118,7 +118,7 @@ cmake -DPython=1 -DPYTHON_EXECUTABLE=$HOME/miniconda3/bin/python -DPYTHON_INCLUD

## Testing

* `make test_run` runs quick tests to check that oxDNA has been correctly compiled, and that the core interactions (`DNA2`, `RNA2` and `DRH`) compute the energy contributions in a nicked double strand correctly.
* `make test_run` runs quick tests to check that oxDNA has been correctly compiled, and that the core interactions (`DNA2`, `RNA2` and `NA`) compute the energy contributions in a nicked double strand correctly.
* `make test_quick` runs longer tests to check that oxDNA works.
* `make test_oxpy` checks that the Python bindings work.
* `make test` runs all sets of tests above.
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2 changes: 1 addition & 1 deletion _sources/observables.md.txt
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Expand Up @@ -106,7 +106,7 @@ Compute and print the hydrogen-bonding (HB) energy of all or selected nucleotide

* `type = hb_energy`: the observable type.
* `[pairs_file = <path>]`: an order parameter file containing the list of pairs whose total HB energy is to be computed.
* `[base_file = <path>]`: file containing a list of nucleotides whose total HB energy is to be computed, one nucleotide per line. If both this option and `pairs_file` are set, the former is silently ignored.
* `[bases_file = <path>]`: file containing a list of nucleotides whose total HB energy is to be computed, one nucleotide per line. If both this option and `pairs_file` are set, the former is silently ignored.

## Hydrogen bonds

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123 changes: 123 additions & 0 deletions _static/_sphinx_javascript_frameworks_compat.js
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