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Add a statement about using confGenerator following #76
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lorenzo-rovigatti committed Oct 20, 2023
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Expand Up @@ -36,6 +36,10 @@ confGenerator <input_file> <box|density> [key1=value1] [key2=value2] [...]

In addition to the input file, *confGenerator* takes another mandatory argument whose meaning depends on its value. It specifies the simulation box if it is a single number larger than 2 (in which case the simulation box is assumed to be cubic) or if it is an x-separated triplet of numbers that specify the length of the edges of the box (which is assumed to be a cuboid). By contrast, the second mandatory argument is interpreted as a number density if it is smaller than 2.

```{warning}
This tool generates a configuration by inserting one particle (nucleotide) at a time, provided that its interaction energy does not exceed some predetermined value (which can be set with `energy_threshold`). It does so by placing each nucleotide randomly, but close to its neighbours, so that it is not too unlikely to end up with a non-overstretched bond. Unfortunately, this procedure makes it extremely unlikely to successfully generate a circular strand.
```

The following examples generate random initial configurations in a cubic box of size 10, in a cuboid of sizes 10x5x15 and in a cubic box with edge $L$ such that $N / L^3 = 0.1$, where $N$ is the total number of nucleotides specified in the topology file.

```text
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