Software...

WAXSiS

WAXSiS - SAXS curves from explicit-solvent MD

We have developed a new web sever called WAXSiS, that computes small- and wide-angle X-ray scattering (SAXS/WAXS) patterns based on explicit-solvent molecular dynamics (MD) simulations. In contrast to previously available methods, WAXSiS provides a highly accurate model for the hydration layer and excluded solvent, and it accounts for thermal fluctuations. Detailed information on how WAXSiS works is given on the WAXSiS site at: http://waxsis.uni-goettingen.de/

 

MemGen

MemGen - setting up membrane simulation systems

We have developed a new web sever called MemGen, that sets up simulation systems of lipid membranes. MemGen is not restricted to specific force fields, lipid types, or MD simulation software. Instead, MemGen works with any uploaded lipid (or amphipilic molecule) in either all-atom or united-atom representation.

Please give it a try (takes only 2 minutes) at http://memgen.uni-goettingen.de/

 

SWAXS image

SAXS/SANS calculations and SAXS-driven MD simulations with a modified GROMACS software

Our modification of GROMACS for (i) computing small- and wide-angle X-ray or neutron scattering curves (SAXS/SANS), small-angle neutron scattering curves (SANS), and for doing SAXS/SANS-driven molecular dynamics simulations is available here.

 

FMA

Functional Mode Analysis

We have developed a new technique called Functional Mode Analysis (FMA) that detects collective motions in biomolecules related to a specific function of the biomolecule. More details on FMA, including the source code of our FMA implementation, is available here, on a separate FMA website. That site also provides a how-to-start tutorial.

 

PDC packed

Setting up a protein-detergent complex

We provide some scripts and help with setting up a simulation system of a protein detergent complex. Please take a look here.

 

 

PDC packed

Influence of ion cloud on the radius of gyration detected by SAXS

We provide a Python script that models a protein as a sphere and uses linearized Poisson-Boltzmann theory to estimate the change in the radius of gyration ΔRg due to the (counter) ion cloud, see here.

 

Pulling the Radius of Gyration with GROMACS

Rg potential

We have written a Gromacs extension that allows you to apply a harmonic (or umbrella-like) restraint along the radius of gyration Rg of a molecule. The source code and some more information is available here.

 

The new g_wham

WHAM bootstrapping example

I have largely rewritten and extended the implementation of the Weighted Histogram Analysis Method (WHAM) that is distributed with the GROMACS simulation software (since version 4.5.2). The implementation, termed g_wham, is thus freely available when you install the Gromacs package.

Note: g_wham does not require that the umbrella simulations were carried out with Gromacs. Non-Gromacs users can provide ASCII input files and use the wide functionality of g_wham.

g_wham supports:

Examples and more details are provided in the following publication. We kindly ask you to cite this reference when you use results generated by g_wham for a publication.
J.S. Hub, B.L. de Groot, and D. van der Spoel
g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates J. Chem. Theory Comput. 6(12), 3713-3720 (2010) [www]