Supercomputer and Chemistry 2

Frontmatter

Supercomputing — What is new

Abstract

The current situation in the supercomputer market is discussed. New manufacturers try to market massively parallel systems. In 1990, several new subsidiaries were founded. On the other hand, the German supercomputer project SUPRENUM was cancelled. As there are no new interesting systems compared to the workshop in 1989, the situation in Japan is discussed in some detail, although the information sources differ in figures, systems and companies. Finally, a list of supercomputer installations in Germany is provided.

U. Harms

Local Area Networks — A Survey

Abstract

The OSI reference model of data communications will be described with respect to local area networks (LANs). A short survey of the two most important, “conventional” LAN architectures, Ethernet and Token-Ring, will be given together with some examples of possible topologies and infrastructures. Then some of the principles and highlights of the relatively new FDDI (Fiber Distributed Data Interface) high-speed LAN will be reported. Finally existing and new types of network applications will be discussed.

G. Michalk

Public Broadband Networks — Present State and Future Perspectives

Abstract

Large-scale technical-scientific Simulations in Supercomputer-Network-complexes, exemplified here by the ‘StuttgartTetrahedron’, represent — among others — one of the scenarios to be extended to a national and eventually European scale in order to guarantee the competitiveness of the continent in the long run. Starting from the Stuttgart experiences the present situation and future alternatives for public broadband networks as a prerequisite for such a geographic extension are investigated.

Paul Christ

Fast Access to Supercomputer Applications

Abstract

Scope of this article is to discuss traditional versus state-of-the-art approaches in high speed data communication featuring the UltraNet™, connecting a variety of supercomputers, mainframes or workstations. Typical network topologies and installation profiles are shown, and one example of a distributed application in the field of chemistry is mentioned. Finally, trends in the rapidly growing network market are analyzed.

K. P. Görtz, K. Schmidt

High Speed Networking Solutions

Abstract

Today, open networking systems based on standards are reshaping the computer and networking industries. This paper discusses some of the ways organizational computing and networking have changed in recent years, what customers are looking for, and how companies like Network Systems are changing and creating a new generation of networking to meet those needs.

J. W. Adams, G. Hemminger

Computational Chemistry in Industry: A Parallel Direct SCF

Abstract

Recent sucessful applications of quantum mechanical SCF-MO calculations at BASF AG show the increasing importance of this method for industrial research and development. However, there Ls a need for improved performance for ab initio SCF calculations. The concepts for a parallel implementation of an ab initio SCF-program are discussed and the expected performance for a cluster of workstations is estimated.

Stefan Brode

Quantum Chemical Investigations of Reactive Intermediates. Carbocations and Alkyl Radicals

Abstract

Using high-level quantum chemical ab initio calculations employing large basis sets and including effects of electron correlation, various small carbocations and alkyl radicals are studied. Equilibrium structures, relative stabilities, harmonic frequencies and potential energy surfaces are determined and, where available, compared to experimental data. The importance of computational methods as a tool complementing experimental approaches for studying short-lived reactive intermediates is stressed.

Wolfram Koch

Long Time Dynamics of Proteins: an off-Lattice Monte Carlo Method

Abstract

A new method is proposed to perform computer simulations of protein dynamics in the long time regime. The method is based on a Monte Carlo technique. The only molecular degrees of freedom considered are bond rotations. All other degrees of freedom including the amide plane torsions are kept rigid. These constraints can approximately account for all interactions related to the chemical bonding. To provide a first test of the method, the non-bonded interactions are turned off in the present application.

An individual Monte Carlo step attempts a local conformational change in a small window of the protein backbone containing 3 residues in consecutive order. The residues outside of the window remain invariant. Ergodicity of the model is demonstrated by comparing exact thermodynamic averages with values obtained from computer simulation data involving 2 × 10⁶ scans of the window along the protein backbone. By relating time with the number of scans of the window along the protein backbone one can evaluate time correlation functions. The end-to-end distance autocorrelation function decays in about 10³-10⁴ scans of the window algorithm. Even in the absence of non-bonded interactions the time decay follows a stretched exponential Kohlrausch decay law.

E. W. Knapp, A. Irgens-Defregger

Quantum Mechanical Calculations of Small Molecules

Abstract

The importance of quantum mechanical calculations as a predictive and analytical tool for chemical research is demonstrated by discussing several research projects of our group.

G. Frenking

Parallel Processing and Computational Chemistry

Abstract

With the increasing use of such methods as dynamic simulations, free energy perturbation and large molecule ab-initio calculations, as well as the use of very elaborate graphical display programs, chemical researchers find increasing frustration in the use of conventional computers to solve their problems. These machines are either too slow or too expensive to be practical for everyday use. However, the advent of parallel computer architectures and parallel algorithms offers a solution to this problem.

Paul Weiner

The Direct IGLO Method for the Calculation of NMR Chemical Shifts with the Program TURBOMOLE

Abstract

The IGLO method for the “ab initio” calculation of NMR chemical shifts is programmed using the two electron integral features of the program package TURBOMOLE. A data flow, optimized implementation on supercomputers makes calculations for large (N≤ 1000 Gaussian basis functions) possible by replacing disk I/O by direct and parallel calculations.

Ulrich Meier

Computer Aided Protein Design: Three Dimensional Model Building of the Saruplase Structure

Abstract

Modelling studies of the three-dimensional structures of the saruplase-domains are presented. The model of the N-terminal EGF-like domain highlights amino acids residues which might be involved in interactions with saruplase specific receptors. The distribution of charged residues on the surface of the kringle-model is different from other kringle- structures. The model structure of the catalytic serine-protease domain points to surface loops, which surround the active site and may participate in interactions with plasminogen. Starting from the structures of the isolated domains a model for the entire enzyme is constructed which is compatible with experimental results.

W. Straßburger, W. Winter, G. J. Steffens, W. A. Günzler, L. Flohé

Backmatter