Software

Fit SAS experiment

Python script fit-experiment developed for WAXSiS allows fitting of experimental SAS intensity curves to modelled (calculated/simulated) intensity curves.

Maciej Wójcik, Jochen Hub

Nov 26, 2023

xmgrace colors

xmgrace is versatile 2D plotting tool. Just the default colors are quite ugly. Here, you find a xmgrace default file with many more defined colors. The colors starting with cb_ are recommended to allow color blind people to understand your scientific plots.

Nov 5, 2023

GROMACS GAFF topologies for 26 steroid compounds

Simulation parameters (topologies) for the General Amber Force Field (GAFF) of 26 typical steroid compounds were derived and refined against experimental membrane/water partition coefficients. On this site, we provide force field topology files in GROMACS format for 26 steroid compounds.

Kalina Atkovska, Jochen Hub

Aug 14, 2018

GROMACS GAFF topologies for 26 steroid compounds

Radius of gyration change $\Delta R_g$ due to the ion cloud of a charged protein

Introduction: influence of the ion cloud of proteins on a SAXS curve SAXS curves report on the overall electron density contrast of a biomolecule with respect to the bulk solvent. The (counter) ion cloud of charged proteins contributes to the electron density contrast, leading to a modified radius of gyration.

Miloš Ivanović, Jochen Hub

Jan 1, 2018

$Radius of gyration change $\Delta R_g$ due to the ion cloud of a charged protein$

GROMACS topology for retinal

Gromacs topology of a retinal bound to lysine via protonated Schiff base Here you find the files required to use gmx pdb2gmx to generate a GROMACS topology of retinal bound to lysine via a protonated Schiff base.

Jochen Hub

Sep 21, 2011

WHAM

The Weighted Histogram Analysis Method (WHAM) is a standard technique used to compute potentials of mean force (PMFs) from a set of umbrella sampling simulations.

Jochen Hub

Nov 16, 2010

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. Given a large set to structures of one protein, for example from a molecular dynamics trajectory, the method detects a collective motion (or collective mode), that is maximally correlated to an arbitrary quantity of interest.

Aug 28, 2009

Pulling the Radius of Gyration with GROMACS

We have written a GROMACS extension that allows you to apply a harmonic (or umbrella-like) restraint along the radius of gyration $R_g$ of a group of atoms (typically molecule).

Aug 28, 2009