TY - GEN A1 - Best, Christoph A1 - Hege, Hans-Christian T1 - Visualizing conformations in molecular dynamics N2 - The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small number of conformations representing essential changes in the shape of the molecule. We present a method to visualize these conformations by point sets in the plane based on a geometrical distance measure between individual configurations. It turns out that different conformations appear as well-separated point sets. The method is further improved by performing a cluster analysis of the data set. The point-cluster representation is used to control a three-dimensional molecule viewer application to show individual configurations and conformational changes. The extraction of essential coordinates and visualization of molecular shape is discussed. T3 - ZIB-Report - SC-98-42 KW - Molecular Dynamics KW - Conformations KW - Visualization KW - Cluster Analysis Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3859 ER - TY - GEN A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Cordes, Frank A1 - Roitzsch, Rainer A1 - Schütte, Christof T1 - From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods N2 - Statistical methods for analyzing large data sets of molecular configurations within the chemical concept of molecular conformations are described. The strategies are based on dependencies between configurations of a molecular ensemble; the article concentrates on dependencies induces by a) correlations between the molecular degrees of freedom, b) geometrical similarities of configurations, and c) dynamical relations between subsets of configurations. The statistical technique realizing aspect a) is based on an approach suggested by {\sc Amadei et al.} (Proteins, 17 (1993)). It allows to identify essential degrees of freedom of a molecular system and is extended in order to determine single configurations as representatives for the crucial features related to these essential degrees of freedom. Aspects b) and c) are based on statistical cluster methods. They lead to a decomposition of the available simulation data into {\em conformational ensembles} or {\em subsets} with the property that all configurations in one of these subsets share a common chemical property. In contrast to the restriction to single representative conformations, conformational ensembles include information about, e.g., structural flexibility or dynamical connectivity. The conceptual similarities and differences of the three approaches are discussed in detail and are illustrated by application to simulation data originating from a hybrid Monte Carlo sampling of a triribonucleotide. T3 - ZIB-Report - SC-98-36 KW - conformational ensemble KW - cluster method KW - structural and dynamical similarity KW - representative KW - conformation KW - essential degrees of freedom KW - transi Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3797 ER - TY - GEN A1 - Best, Christoph T1 - A simple C++ library for manipulating scientific data sets as structured data N2 - Representing scientific data sets efficiently on external storage usually involves converting them to a byte string representation using specialized reader/writer routines. The resulting storage files are frequently difficult to interpret without these specialized routines as they do not contain information about the logical structure of the data. Avoiding such problems usually involves heavy-weight data format libraries or data base systems. We present a simple C++ library that allows to create and access data files that store structured data. The structure of the data is described by a data type that can be built from elementary data types (integer and floating-point numbers, byte strings) and composite data types (arrays, structures, unions). An abstract data access class presents the data to the application. Different actual data file structures can be implemented under this layer. This method is particularly suited to applications that require complex data structures, e.g. molecular dynamics simulations. Extensions such as late type binding and object persistence are discussed. T3 - ZIB-Report - TR-98-06 KW - scientific file formats KW - structured data KW - object persistence Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5674 ER -