> For the complete documentation index, see [llms.txt](https://ehjc.gitbook.io/kallisto/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://ehjc.gitbook.io/kallisto/features/vdw.md).

# van-der-Waals Radii

Calculate atomic van der Waals radii.

## Introduction

Atomic van-der-Waals (vdW) radii are calculated from atomic polarizabilities as recently introduced by Fedorov *et al.* (see their [arXiv](https://arxiv.org/abs/1803.11507)). In their work, they obtained a quantum-mechanical relation between atomic polarizabilities and vdW radii.

$$
R\_{vdw}(\alpha) = \theta\_a \alpha^{1/7},
$$

where `thetaa = 2.54` has been obtained by fitting to reference data for noble gases. Since the present model should be easily applicable to all elements up to Radon, an additional element-wise parameter `thetab` is introduced and fitted to reproduce theoretically determined vdW radii (see works of [Rahm](https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/chem.201602949) and [Mantina](https://pubs.acs.org/doi/10.1021/jp8111556)).

$$
R\_{vdw}(\alpha) = \theta\_a \theta\_b\alpha^{1/7}
$$

We apply static atomic polarizabilities for the calculation of vdW radii. The graphic below depicts calculated vdW radii (`vdwtype=rahm`) for all atoms up to Radon (CN = 0, q = 0).

![](https://3403678501-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-MP5mmUxq5nIfLRvFnya%2Fsync%2F6914c9984dda57d7759e961ddfd3c5526c3da0e6.png?generation=1610813171745376\&alt=media)

## Define the Subcommand

{% tabs %}
{% tab title="vdw" %}

```bash
> kallisto vdw options arguments
```

{% endtab %}

{% tab title="options" %}

```markup
--chrg <int>
(optional, default: 0)
description:
 absolute charge (qtotal) of the input structure (Lagrangian constraint)

 --vdwtype <string>
 (optional, default: rahm)
 description:
  reference atomic van der Waals radii
   rahm: 10.1002/chem.201700610
   truhlar: 10.1021/jp8111556

--angstrom (flag)
(optional, default: false)
description:
 calculate van-der-Waals radii in Ångström
 
--out <string> 
(optional)
description: 
 write output to file
```

{% endtab %}

{% tab title="arguments" %}

```
input file is given as (positional) argument
```

{% endtab %}
{% endtabs %}

## Application

To calculate atomic van-der-Waals radii for a neutral charged Alanine-Glycine molecule, we call the subcommand `vdw`

```bash
> kallisto vdw alanine-glycine.xyz
3.3065606171598922
3.38164759676716
3.4391750162303536
3.311855692814488
3.3790680338248973
3.2967634203187104
3.4727151121721547
3.2976318319108247
3.3094215076503897
2.420916892530216
2.4135730093586507
3.356462625678808
2.5457085831894677
2.4274072320381417
2.5251614207290154
2.527093029228339
2.409141369050233
2.540154025796337
2.536646925483585
2.5536833297719026
# Save output to file 'vdw'
> kallisto vdw --out vdw alanine-glycine.xyz
3.3065606171598922
3.38164759676716
3.4391750162303536
3.311855692814488
3.3790680338248973
3.2967634203187104
3.4727151121721547
3.2976318319108247
3.3094215076503897
2.420916892530216
2.4135730093586507
3.356462625678808
2.5457085831894677
2.4274072320381417
2.5251614207290154
2.527093029228339
2.409141369050233
2.540154025796337
2.536646925483585
2.5536833297719026
```

Now we obtain a list of atomic van-der-Waals radii. However, we can furthermore calculate van-der-Waals radii for the cationic (or anionic) Alanine-Glycine molecule by incorporating the `chrg` option as described in the subcommand definition.