SAXS/WAXS calculations using all-atom MD simulations

SWAXS image

On these sites, we provide a modified source code of GROMACS for the analysis of small- and wide-angle X-ray scattering data (SWAXS). The code may be used to

Source code

The current source code is an extension of GROMACS 4.62 available here: gromacs_4.62_swaxs_v0.2.tar.gz

For compiling the code, please follow the instructions on the Gromacs website for compiling 4.6 versions. Please note that this code is not official Gromacs, hence the Gromacs developers are not responsible for this extension.
License: The code is distributed under the GNU Lesser General Public License (LGPL).

Previous versions: gromacs_4.62_swaxs_v0.1.tar.gz

Web server

WAXSiS

Note our web server: For computing only a few SWAXS curves our web server WAXSiS may be more suitable. WAXSiS runs a short explicit-solvent MD simulation from an uploaded PDB structure and subsequently computes the SWAXS curve. WAXSiS also allows the upload of a trajectory file. For more extensive calculations, however, the webserver gets cumbersome, hence you may better download the code and run the calculations on your computer.

Documentation and tutorials

The documentation for our SAXS-extended Gromacs is still rudimentary. A list of SWAXS-related mdp options and tutorials is provided on a separate documentation site. If you run into problems, please do not hesitate to contact us. We want you to use our software, so we're happy to help.

Relevant publications

For SWAXS curve predictions from an MD simulations:
Validating solution ensembles from molecular dynamics simulation by wide-angle X-ray scattering data
Po-chia Chen and Jochen S. Hub
Biophys. J., 107, 435-447 (2014) [pdf] [www] [supporting info] [main text and supporting info]

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics
Christopher J. Knight and Jochen S. Hub
Nucleic Acids Res., 43, W225-W230 (2015) [www] [pdf]

For SWAXS-driven MD simulations (structure refinement against SWAXS curves):
Interpretation of solution X-ray scattering data by explicit-solvent molecular dynamics
Po-chia Chen and Jochen S. Hub
Biophys. J., 108, 2573–2584 (2015) [pdf] [www] [supporting info] [main text and supporting info]

Bayesian structure and ensemble refinement against SAXS data:
Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics
Roman Shevchuk and Jochen S. Hub
PLoS Comp. Biol., 13, e1005800 (2017) [www] [pdf]

Other relevant publications:
Structural properties of protein-detergent complexes from SAXS and MD simulations
Po-chia Chen and Jochen S. Hub
J. Phys. Chem. Lett., 6, 5116–5121 (2015) [www] [pdf] [supporting info]

Ultrafast anisotropic protein quake propagation after CO-photodissociation in myoglobin
Levin U.L. Brinkmann and Jochen S. Hub
Proc. Natl. Acad. Sci. USA, 113, 10565–10570 (2016) [www] [pdf] [pdf+supporting info]

Anisotropic time-resolved solution X-ray scattering patterns from explicit-solvent molecular dynamics
Levin U.L. Brinkmann and Jochen S. Hub
J. Chem. Phys., 143, 104108 (2015) [www] [pdf]

Temperature-dependent atomic models of detergent micelles refined against small-angle X-ray scattering data
Miloš T. Ivanović, Linda Bruetzel, Jan Lipfert, and Jochen S. Hub
Angew. Chem. Int. Ed., 57, 5635-5639 (2018) [www] [pdf] [supporting info]