gmx-scattering

Intro

This is implementation of gmx scattering module that is aimed to replace old gmx sans and gmx saxs modules. Module gmx scattering uses Debye method to calculate SANS and SAXS spectra via pair distance distribution histogram.

$$I(s) = \sum_{i} \sum_{j} f_{i}(s) * f_{j}(s) * \frac{sin(s * r_{ij})}{s * r_{ij}}$$

where $r_{ij} = \left| \vec{r_{i}} - \vec{r_{j}} \right|$ is distance between atoms $i$ and $j$ and $f_{i}(s)$, $f_{j}(s)$ are atomic structure factors for atoms $i$ and $j$

For SAXS mode gmx scattering uses Cromer-Mann approximation for atomic structure factors

$$s(q) = \sum_{i}^{4} a_{i} * \exp(- b_{i} * (\frac{q}{4\pi})^2) + c$$

Installation

• Install GROMACS (you need version 2022.x or 2023.x)
• clone this repo and build it with cmake