Richard Grunzke

The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations

The MoSGrid portal offers an approach to carry out high-quality molecular simulations on distributed compute infrastructures to scientists with all kinds of background and experience levels. A user-friendly Web interface guarantees the ease-of-use of modern chemical simulation applications well established in the field. The usage of well-defined workflows annotated with metadata largely improves the reproducibility of simulations in the sense of good lab practice. The MoSGrid science gateway supports applications in the domains quantum chemistry (QC), molecular dynamics (MD), and docking. This paper presents the open-source MoSGrid architecture as well as lessons learned from its design.

Insights into the influence of dispersion correction in the theoretical treatment of guanidine-quinoline copper(I) complexes

For the description of steric effects, dispersion correction is important in density functional theory. By investigation of sterically encumbered guanidine‐quinoline copper bis(chelate) complexes, we could show that the correct description requires modern dispersion correction using Becke–Johnson (BJ) damping and that earlier dispersion corrections are not sufficient. The triple‐zeta basis set def2‐TZVP of the Ahlrichs series is balanced and converged for the structural description. With regard to functionals, the best structural description is obtained with the TPSSh functional but B3LYP is very suited as well. Cutting of ligand substituents leads to distortions which limit the predictive ability of such calculations. We recommend the calculation of “full” chemical systems with inclusion of dispersion correction using BJ damping. In the further analysis of the regarded copper bis(chelate) complexes, we found that the theoretical description of optical and Raman spectra is not much affected by the dispersion although charge transfer excitations come into play and that B3LYP/def2‐TZVP is the best choice. Hence, we can derive the result that the correct structural description with dispersion serves as crucial basis for subsequent calculation steps.

A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics

Structural bioinformatics applies computational methods to analyze and model three-dimensional molecular structures. There is a huge number of applications available to work with structural data on large scale. Using these tools on distributed computing infrastructures (DCIs), however, is often complicated due to a lack of suitable interfaces. The MoSGrid (Molecular Simulation Grid) science gateway provides an intuitive user interface to several widely-used applications for structural bioinformatics, molecular modeling, and quantum chemistry. It ensures the confidentiality, integrity, and availability of data via a granular security concept, which covers all layers of the infrastructure. The security concept applies SAML (Security Assertion Markup Language) and allows trust delegation from the user interface layer across the high-level middleware layer and the Grid middleware layer down to the HPC facilities. SAML assertions had to be integrated into the MoSGrid infrastructure in several places: the workflow-enabled Grid portal WS-PGRADE (Web Services Parallel Grid Runtime and Developer Environment), the gUSE (Grid User Support Environment) DCI services, and the cloud file system XtreemFS. The presented security infrastructure allows a single sign-on process to all involved DCI components and, therefore, lowers the hurdle for users to utilize large HPC infrastructures for structural bioinformatics.

Standards-based metadata management for molecular simulations

State‐of‐the‐art research in a variety of natural sciences depends heavily on methods of computational chemistry, for example, the calculation of the properties of materials, proteins, catalysts, and drugs. Applications providing such methods require a lot of expertise to handle their complexity and the usage of high‐performance computing. The MoSGrid (molecular simulation grid) infrastructure relieves this burden from scientists by providing a science gateway, which eases access to and usage of computational chemistry applications. One of its cornerstones is the molecular simulations markup language (MSML), an extension of the chemical markup language. MSML abstracts all chemical as well as computational aspects of simulations. An application and its results can be described with common semantics. Using such application, independent descriptions users can easily switch between different applications or compare them. This paper introduces MSML, its integration into a science gateway, and its usage for molecular dynamics, quantum chemistry, and protein docking. Copyright

Quantum chemical meta-workflows in MoSGrid

Quantum chemical workflows can be built up within the science gateway Molecular Simulation Grid. Complex workflows required by the end users are dissected into smaller workflows that can be combined freely to larger meta‐workflows. General quantum chemical workflows are described here as well as the real use case of a spectroscopic analysis resulting in an end‐user desired meta‐workflow. All workflow features are implemented via Web Services Parallel Grid Runtime and Developer Environment and submitted to UNICORE. The workflows are stored in the Molecular Simulation Grid repository and ported to the SHIWA repository. Copyright

Meta-Metaworkflows for Combining Quantum Chemistry and Molecular Dynamics in the MoSGrid Science Gateway

MoSGrid (Molecular Simulation Grid) is a user-friendly and highly efficient science gateway which contains three domains for the different methodologies used in chemistry: quantum chemistry, molecular dynamics, and docking. Workflows are implemented by using the WS-PGRADE technology. By adding an abstraction layer, we are able to develop meta-metaworkflows for quantum chemical applications and a combination between quantum chemical and molecular dynamics applications. This approach allows researchers to easily and more quickly create highly complex workflows allowing them to shorten the time-to-result considerably.

Copper Guanidinoquinoline Complexes as Entatic State Models of Electron-Transfer Proteins

The electron-transfer abilities of the copper guanidinoquinoline (GUAqu) complexes [Cu(TMGqu)2 ]+/2+ and [Cu(DMEGqu)2 ]+/2+ (TMGqu=tetramethylguanidinoquinoline, DMEGqu=dimethylethylguanidinoquinoline) were examined in different solvents. The determination of the electron self-exchange rate based on the Marcus theory reveals the highest electron-transfer rate of copper complexes with pure N-donor ligands (k11 =1.2×104  s-1  m-1 in propionitrile). This is supported by an examination of the reorganisation energy of the complexes by using Eyring theory and DFT calculations. The low reorganisation energies in nitrile solvents correspond with the high electron-transfer rates of the complexes. Therefore, the [Cu(GUAqu)2 ]+/2+ complexes act as good entatic states model of copper enzymes. The structural influence of the complexes on the kinetic parameters shows that the TMGqu system possesses a higher electron-transfer rate than DMEGqu. Supporting DFT calculations give a closer insight into the kinetics and thermodynamics (Nelsens four-point method and isodesmic reactions) of the electron transfer.

UNICORE 7 — Middleware services for distributed and federated computing

UNICORE is a mature middleware solution for building federated computing and data infrastructures (i.e. Grids), providing access to high-performance computing (HPC), clusters, file systems and other resources. This paper presents the state of the art in UNICORE, focusing on several major improvements that have been implemented for version 7 released in 2015. We have added RESTful APIs to UNICORE, allowing to easily create applications integrating the full range of UNICORE enabled data and compute resources. New features for data processing and analysis have been added. A new web portal allows simple web access. We have simplified the end-user experience by removing the requirement for X.509 certificates, establishing certificate-less authentication and trust delegation mechanisms. A new component, Unity, for identity management is presented, which enables a wide range of integration scenarios including SAML federations and OpenID connect.

Using Science Gateways for Bridging the Differences between Research Infrastructures

Researchers can perform large-scale analyses on diverse computing and data infrastructures such as NGIs (National Grid Infrastructures), XSEDE (Extreme Science and Engineering Discovery Environment) and PRACE (Partnership for Advanced Computing in Europe). Some are national like NGIs and XSEDE, some are international like PRACE and all of them require a more or less restrictive application process to get access to resources. Science gateways integrating diverse infrastructures provide the possibility to re-use methods independent of such underlying infrastructures and thus potentially deliver the technical prerequisite for creating reproducible science. To achieve this goal, science gateways have to be integrated seamlessly with security mechanisms and job, data as well as workflow management of the targeted resources. This paper gives an overview on general findings for porting science gateways as well as the challenges faced for porting the German MoSGrid science gateway (Molecular Simulation Grid) to exploit XSEDE and PRACE infrastructures.

Performance Studies on Distributed Virtual Screening

Virtual high-throughput screening (vHTS) is an invaluable method in modern drug discovery. It permits screening large datasets or databases of chemical structures for those structures binding possibly to a drug target. Virtual screening is typically performed by docking code, which often runs sequentially. Processing of huge vHTS datasets can be parallelized by chunking the data because individual docking runs are independent of each other. The goal of this work is to find an optimal splitting maximizing the speedup while considering overhead and available cores on Distributed Computing Infrastructures (DCIs). We have conducted thorough performance studies accounting not only for the runtime of the docking itself, but also for structure preparation. Performance studies were conducted via the workflow-enabled science gateway MoSGrid (Molecular Simulation Grid). As input we used benchmark datasets for protein kinases. Our performance studies show that docking workflows can be made to scale almost linearly up to 500 concurrent processes distributed even over large DCIs, thus accelerating vHTS campaigns significantly.