Bio-Lab
You can contact the LRZ Bio-Lab at biolab@lrz.de.
Summer of Simulation
The LRZ invited Master and PhD Students, starting in the field of simulation and supercomputing for the "Summer of Simulation" (SoS). The goal of this training program is to develop a scalable and optimal setup for applications from the fields of molecular dynamics, quantum chemistry or bioinformatics and run them on SuperMUC during the summer months. SoS participants could acquire a budget of up to 10 Mio CPU hours in the following two stage process.
Applicants had to write a short proposal (about 1 page) describing their project, their experience with simulation and supercomputing, contact data and affiliation and send it to LRZ. Selected proposals were assigned a tutor from the LRZ Bio-Lab. In the first stage, each project was granted 1Mio CPU hours on SuperMUC to develop and test a scalable setup of her/his application together with the tutor. In the second stage, the projects could apply for an additional 9 Mio CPU hours. In a final meeting, all participants shared their results.
Summer of Simulation 2018 (SoS18)
| Title of project | Application |
|---|---|
Semiconducting Metal-Organic Frameworks as Sensor Materials. Virtual Screening of a Vast Candidate Space | FHI-AIMS, CP2K, FireWorks workflow manager |
Computational screening of transition metal oxide catalysts for cost-effective hydrogen fuel production | CP2K, Gaussian |
Probing the Dynamics of Photoexcited Biomolecules in their Natural Environment at the Quantum Level | ChemShell 3.7.0 , LSDalton 1.3 |
| Computational High-Throughput Screening for Mapping Chemical Space | VASP, LAMMPS |
Development of a Neural Network Potential for Lithium Manganese Oxides in Water | DFT - NNP (Neural Network Potential) - CP-PAW |
Conformational dynamics of alpha-Secretase studied by free energy si | Amber16 |
Multi-scale simulations on charge separation in Photosystem II | Turbomole and NAMD |
The Protein Recycling Machinery of the Cell | Orca and NAMD |
Dynamics of basal dislocations in bilayer graphene | LAMMPS |
Summer of Simulation 2017 (SoS17)
| Title of project | Application |
|---|---|
| Optimization of the HADES dielectric continuum model for biomolecular simulations | Iphigenie |
| Drug design/structure prediction of a metallo protein | Amber |
Photocatalytic water-splitting with carbon nitride materials: Combining the condensed matter and molecular approaches | CP2k, QE |
Binary doping of HfO2 and ZrO2 to improve the piezoelectric properties | Abinit, Aims, QE |
| Molecular dynamics free energy simulations on contacts in protein crystals | Gromacs, Amber |
Ab initio modelling of iridium oxide nanoparticles as catalysts for proton exchange membrane water electrolysis cells | Aims, CP2k |
Replica exchange simulation of the switching process in small GTPases | Amber |
| Deactivation of Hazardous Chemicals at Oxide Surfaces | CPMD |
| Computer-aided optimization of the CIGS deposition process in the industrial implementation | AKMC |
Summer of Simulation 2016 (SoS16)
| Titel of project | Application |
|---|---|
| Hubbard-corrected ab initio molecular dynamics for oxide materials | cpmd |
| Enzyme design by QM/MM Monte Carlo | namd, turbomole |
| Ab-initio electronic structure calculation of equilibrated real size chalcopyrite nano-particles in aqueous solution | vasp |
| Domain dynamics of Hsp90 studied by free energy simulations | amber16, umbrella REMD |
| Experimentally-Informed Large-Scale Atomistic Simulations of Nanoporous Gold | lammps, ovito |
| Functionalization of Oxide Surfaces from the Liquid: Chemical Reactions at the Solid/Liquid Interface | cpmd, multiple walker |
| Chemical Reactivity of Amorphous Oxide Surfaces | cpmd |
| Cu / ZnO neural-network interaction potentials | vasp, neural network Forcefield |