Department home Homepage Institute Disclaimer Site Map Research Projects Gallery Publications Staff Jobs PhD programs Teaching & Conferences Downloads Contact Theoretical and Methods Advancements     / home / Research Projects / Methods / g_permute: A PRPCA Implementation 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 ... Theory of Dynamic Force Spectroscopy Recent advances in atomic force microscopy, biomembrane force probe experiments, and optical tweezers allow to measure the response of single molecules to mechanical stress with high precision. Such experiments, due to limited spatial resolution, typically access only ... Streptavidin Biotin Unbinding Simulation The force required to rupture the streptavidin-biotin complex has been calculated by computer simulations. The computed force agrees well with that obtained by recent single molecule atomic force microscope experiments. The simulations suggest a multiple-pathway rupture ... 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 ... [more] Constant pH molecular dynamics simulations Typically, in a molecular dynamics simulation, the protonation states of ionizable groups of a protein are set in the beginning of the simulation. This is not always an obvious task, in particular for histidine, as its pKa is close to the physiological pH. In contrast, ... [more] CGI – Accurate free energy differences from nonequilibrium simulations The molecular-dynamics-based calculation of accurate free energy differences for biomolecular systems is a challenging task. We suggest and assess a new nonequilibrium free energy method, Crooks Gaussian Intersection (CGI), which combines the advantages of existing ... [more] Optimized Scaling for GROMACS Simulations of big molecular dynamics systems can easily occupy a compute cluster for weeks or even months. Continuous efforts are being made to ensure that our computer power is used most efficiently. This includes network fine-tuning and code optimization to reach the ... [more] Predicting Unimolecular Chemical Reactions: Chemical Flooding The calculation of reaction pathways, energy barriers and reaction rates for chemical reactions of small molecules is a routine task in todays theoretical quantum chemistry. Established methods exist for tasks like (a) minimization of educt states, (b) exploring ... [more] Predicting Conformational Transitions: Conformational Flooding We present a method to predict complex structural (conformational) transitions in irregular or disordered macromolecular systems, such as proteins or glasses, at the atomic level. Our method aims at rare events, which currently cannot be predicted with traditional ... [more] Conformational dynamics of proteins Proteins are polypeptides which consist of typically 50 to several 100 amino acids and fold into protein-specific three-dimensional structures. This native structure is determined by the amino acid sequence of a protein, which is genetically encoded. [more] Flooding in Gromacs: Accelerated barrier crossings in molecular dynamics The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that due to the enormous computational effort involved only processes at nanoseconds to microseconds time scales or faster can be studied directly. Unfortunately, apart from a few ... [more] © 2011, Max Planck Institute for Biophysical Chemistry, Göttingen