Hünfeld 2024: Workshop on Computer Simulation and Theory of Macromolecules

Hünfeld 2024: Workshop on Computer Simulation and Theory of Macromolecules

April 19-20, 2024

Thank you all for your contribution to this year’s workshop! See you all back again in 2025!

Friday, April 19, 2024 Times given in Central European Summer Time (UTC+2)

11:00 – 13:00

 Arrival, registration and lunch

13:00 – 13:05


Chair Ilja Solov’yov
13:05 – 13:30 Rita Ann Roessner (University of Montpellier, France)
Exploring the Conformational Landscape of a Class A G Protein-Coupled Receptor with
Biased Molecular Dynamics Simulations and Markov State Modeling
13:30 – 13:55
Saha Satvati (Instituto Italiano di Tecnologia, Genoa, Italy)
Molecular Dynamics Simulations of Bacterial Membrane Interaction with Double and
Tetra Branched Antimicrobial Peptides
13:55 – 14:20 Katharina Spies (Karlsruhe Institute of Technology, Germany)
Proton Coupled Electron Transfer in Biomimetic Peptides
14:20 – 14:45 Daniel Szöllösi (Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany)
Simulation of Ion Mobility Spectrometry Experiments
14:45 – 15:10 Saumyak Mukherjee (Ruhr University Bochum, Germany)
Microscopic Dynamics of an Intrinsically Disordered Protein in a Condensate
15:10 – 15:25

Coffee break

Chair Sara Gabrielli
15:25 – 15:50  Sanjoy Paul (Max Planck Institute of Biophysics, Frankfurt, Germany)
Delineating the Shape of COPII Coated Membrane Bud
15:50 – 16:15 Arya Changiarath Sivadasan (Johannes Gutenberg University, Mainz, Germany)
Condensate Coexistence in Gene Transcription: Molecular Dynamics Insights
16:15 – 16:40 Aleksandr Zlobin (Leipzig University, Germany)
Charges and Boundary Terms: Easy Ways to Spoil Your QM/MM(MD) Results
16:40 – 17:05 Isabell Louise Grothaus (University of Bremen, Germany)
The Third Dimension of the Sugar Code under the Computational Microscope
17:05 – 17:30 Marius Trollmann (Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany)
One Ring to Rule Them All: Lugdunin’s Disruptive Effects
17:30 – 17:55 Patrick Quoika (Technical University of Munich, Germany)
Evaporation Behavior of Common Water Models in Molecular Dynamics Simulations
18:00 – 19:00


19:30 –20:30

Poster Presentations: odd numbers/ Beer

20:30 – 21:30

 Poster Presentations: even numbers/ Beer

Saturday, April 20, 2024 Times given in Central European Summer Time (UTC+2)

 8:00 – 8:50


Chair Helmut Grubmüller
8:55 –   9:35 Invited Speaker: Pavel Jungwirth (IOCB Prague, Czech Republic)
Charge Scaling Force Fields for Biomolecular Simulations: Do Free Lunches Exist?
Chair Katharina Scherer
 9:35 – 10:00 Steffen Schultze (Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany)
Bayesian Electron Density Determination from Single-Molecule X-ray Scattering
10:00 – 10:25 Leif Seute (Heidelberg Institute for Theoretical Studies, Germany)
Learning a State of the Art MM Force Field
10:25 – 10:45

Coffee break

Chair Lars Schäfer
10:45 – 11:10 Sudarshan Behera (Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany)
Understanding Errors in Relative Binding Free Energy Calculations
11:10 – 11:35 Alejandro Martínez-León (Saarland University, Saarbrücken, Germany)
Absolute Binding Free Energy Calculations: A Systematic Force Field Comparison by a Newly Designed Computational Pipeline
11:35 – 12:00 Ahmed Ali (University of Freiburg, Germany)
Allosteric Communication in PDZ3 Studied by Nonequilibrium Simulations and Markov State Model
12:00 - 13:00


Chair Kateryna Lohachova
13:00 – 13:25 Mislav Brajković (Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany)
Investigation of Effect of Loop Motion on the Residence Time of Histamine-1-Receptor (H1R) Antagonists by τRAMD
13:25 – 13:50 Chenggong Hui (Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany)
Effects of Charge Scaling on Potassium Channel Simulations, Conductance, Ion Occupancy, Voltage Response, and Selectivity
13:50 – 14:15 Lisa Sophie Kersten (Heinrich Heine University, Düsseldorf, Germany)
Atomistic Mechanism of Copper Transfer to Plant Receptor ETR and Structural Receptor Dynamics after Binding of Ethylene and 1-Methylcyclopropene
14:15 – 14:40 Jonathan Hungerland (Carl von Ossietzky University, Oldenburg, Germany)
Introducing the Automated Ligand Searcher
14:40 – 15:05 Sara Gabrielli (Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany)
Rest Assured: Programmed Translational Stalling Studied by Means of MD Simulations
15:05 – 15:20

Coffee break

Chair Rainer Böckmann
15:20 – 15:45 Chetan Poojari (Saarland University, Saarbrücken, Germany)
Molecular Mechanisms Unveiling Virus-Host Interactions Steering Membrane Fusion
15:45 – 16:10 Yanna Gautier (CNRS, Paris, France)
High-Pressure Response of the Coupled Dynamics of Lipids and Membrane Proteins
16:10 – 16:35 Beatrice Caviglia (Université de Paris Cité, University of Perugia, Paris, France)
Investigation on the Protein Dynamics at Extreme Temperatures
16:35 – 17:00 Gustavo Enrique Olivos Ramirez (Institute of Fundamental Technological Research, Polish
Academy of Sciences, Warsaw, Poland)

Accessing the Conformational Space of Viral Protein Models by GōMartini 3 Approach
17:00 – 17:25 Balázs Fábián (Max Planck Institute for Biophysics, Frankfurt am Main, Germany)
Molecular Modeling of the SARS-CoV-2 Nucleocapsid Protein Using Martini
17:30 – 17:55

Poster prize, final remarks




Dear biophysics friends,

Also in 2024 we will organize our 'Computer Simulation and Theory of Macromolecules' workshop to discuss recent advances in theory and application of biomolecular simulations. As usual, our aim is to promote and facilitate the exchange among the biomolecular theory and simulation communities of Germany and beyond. By organizing the workshop in a hybrid format, we strive to be most inclusive also for attendees who might find travelling difficult, and hope for lively discussions and knowledge exchange both on-site and online!

We therefore cordially invite you all and in particular students and postdocs to participate in the upcoming meeting on April 19-20, 2024!

As invited speaker during the 2024 workshop, we gladly announce our colleague and friend Pavel Jungwirth, Professor at the Charles University in Prague, and Chair of the Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences. He will give us insights into his field of expertise with the talk "How can cell penetrating peptides enter via membrane fusion?"

As is tradition, the meeting will be held in the Hünfeld Monastery right in the center of Germany. We will offer a poster session on-site on Friday evening. The virtual option will allow for joining the presentations via a video conferencing tool. We will offer a poster session on-site on Friday evening for a limited number of posters, and will provide a virtual poster gallery including posters from virtual and on-site participants.

We consider it an important feature of the workshop to offer affordable accommodations and meals to make it easier for students, graduate students, and postdocs to attend on-site. In case accommodation at the Hünfeld Monastery is already fully booked at the time of your registration, we will kindly ask you to organize your accommodation externally by yourself. Online participation is free of charge.

If you have any further questions about the workshop, please contact the workshop office and send an E-Mail to theory-workshop@mpinat.mpg.de

With our best regards,

Volkhard Helms, Helmut Grubmüller

Further information

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