Department home Homepage Institute Disclaimer Site Map Research Projects Gallery Publications Staff Jobs PhD programs Teaching & Conferences Downloads Contact Software Developed in the Grubmüller Lab     / home / Downloads / g_permute Biomolecular processes are governed by free energy changes and thus depend on a fine-tuned interplay between entropy and enthalpy. To calculate accurate values for entropies from simulations is particularly challenging for the solvation shell of proteins, which ... [more] FRETsg FRETsg is a tool for a fast qualitative analysis of multiple FRET (fluorescence resonance energy transfer) experiments. FRET experiments principally yield the distances between fluorescent dyes, which are commonly used for labelling proteins, DNA, RNA, etc. If multiple ... [more] FretTrace Single molecule Fluorescence Resonance Energy Transfer (FRET) experiments are a powerful and versatile tool for studying conformational motions of single biomolecules at a millisecond time scale. Typically, the small number of recorded photons limits the achieved time ... [more] EGO EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, under PARIX and inhomogeneous clusters of UNIX workstations under PVM or ... [more] Solvate Solvate is a program to construct an atomic solvent environment model for a given atomic macromolecule for the use in an MD simulation. Solvate generates irregularly-shaped solvent volumes, adapted to a given solute's structure. It allows efficient computation of ... [more] Full Correlation Analysis of Conformational Protein Dynamics Collective coordinates for protein motions, can be extracted from MD simulations with established methods, mainly via calculation of the covariance matrix and subsequent principal component analysis[1]. This established approach, however, relies on quasi-harmonic ... [more] Cutlat Cutlat determines inter-repeat curvature, twist and lateral bending angles, as well as their full-length sums for multi-repeat unit proteins, including e.g. LRR, Armadillo, HEAT or ankyrin repeat proteins. As the principal axes of repeats are used for the calculation ... [more] MD Benchmark Diese Seite enthält Dateien für die Bewerber auf die Cluster-Ausschreibung des Jahres 2011. Neben der zu benutzenden Quellcode-Version ist auch das für den Benchmark benötigte Eingabefile hier abgelegt. Zusätzlich finden sich Hinweise zur Übersetzung des Quellcodes und ... [more] Generalized Correlation for Biomolecular Dynamics Correlated motions in biomolecules, in particular proteins, are ubiquitous and often essential for biomolecular function. Correct assessment of correlated motions, both experimentally and from theory and simulations, is therefore crucial for a quantitative understanding ... © 2011, Max Planck Institute for Biophysical Chemistry, Göttingen