SAXS/WAXS/SANS calculations using all-atom MD simulations

On these sites, we provide a modified source code of GROMACS for the analysis of small- and wide-angle X-ray scattering data (SWAXS) as well as small-angle neutron scattering data (SANS). The code may be used to
- Compute SWAXS/SANS curves using all-atom explicit-solvent MD simulations, and
- to carry out SWAXS/SANS-driven simulations, i.e., to carry out structure refinement against SWAXS/SANS data using MD simulations.
Source code
The current source code is an extension of GROMACS 2021.5 and is
available at GitLab.
For compiling the code, please follow the documentation at GitLab. 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 (not recommended): gromacs_4.62_swaxs_v0.1.tar.gz, gromacs_4.62_swaxs_v0.2.tar.gz
Web server

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 is available at GitLab. 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
Overview articles:
Leonie Chatzimagas and Jochen S. Hub
Submitted to Meth. Enzymol., edited by John Tainer.
bioRxiv
[www]
Leonie Chatzimagas and Jochen S. Hub
Submitted to Meth. Enzymol., edited by John Tainer.
arXiv
[www]
For SWAXS/WAXS curve predictions from an MD simulations:
Po-chia Chen and Jochen S. Hub
Biophys. J., 107, 435-447 (2014)
[pdf]
[www]
[supporting info]
[main text and supporting info]
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):
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:
Roman Shevchuk and Jochen S. Hub
PLoS Comp. Biol., 13, e1005800 (2017)
[www]
[pdf]
Maximum-entropy ensemble-refinement against SAXS data:
Markus R. Hermann and Jochen S. Hub
J. Chem. Theory Comput., 15, 95103-5115 (2019)
[www]
[pdf]
[supporting info]
Other relevant publications:
Po-chia Chen and Jochen S. Hub
J. Phys. Chem. Lett., 6, 5116–5121 (2015)
[www]
[pdf]
[supporting info]
Levin U.L. Brinkmann and Jochen S. Hub
Proc. Natl. Acad. Sci. USA, 113, 10565–10570 (2016)
[www]
[pdf]
[pdf+supporting info]
Levin U.L. Brinkmann and Jochen S. Hub
J. Chem. Phys., 143, 104108 (2015)
[www]
[pdf]
Miloš T. Ivanović, Linda Bruetzel, Jan Lipfert, and Jochen S. Hub
Angew. Chem. Int. Ed., 57, 5635-5639 (2018)
[www]
[pdf]
[supporting info]