TY - GEN A1 - Bujotzek, Alexander A1 - Schütt, Ole A1 - Nielsen, Adam A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Efficient Conformational Analysis by Partition-of-Unity Coupling T2 - Math Chem N2 - Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent. T3 - ZIB-Report - 13-58 KW - Markov State Models KW - Meshfree KW - Molecular Simulation KW - Partition of Unity Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42570 SN - 1438-0064 ER - TY - GEN A1 - Götschel, Sebastian A1 - von Tycowicz, Christoph A1 - Polthier, Konrad A1 - Weiser, Martin T1 - Reducing Memory Requirements in Scientific Computing and Optimal Control N2 - In high accuracy numerical simulations and optimal control of time-dependent processes, often both many time steps and fine spatial discretizations are needed. Adjoint gradient computation, or post-processing of simulation results, requires the storage of the solution trajectories over the whole time, if necessary together with the adaptively refined spatial grids. In this paper we discuss various techniques to reduce the memory requirements, focusing first on the storage of the solution data, which typically are double precision floating point values. We highlight advantages and disadvantages of the different approaches. Moreover, we present an algorithm for the efficient storage of adaptively refined, hierarchic grids, and the integration with the compressed storage of solution data. T3 - ZIB-Report - 13-64 KW - optimal control KW - trajectory storage KW - mesh compression KW - compression Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42695 SN - 1438-0064 ER - TY - GEN A1 - Krause, Dorian A1 - Fackeldey, Konstantin A1 - Krause, Rolf T1 - A parallel multiscale simulation toolbox for coupling molecular dynamics and finite elements N2 - It is the ultimate goal of concurrent multiscale methods to provide computational tools that allow to simulation physical processes with the accuracy of micro-scale and the computational speed of macro-scale models. As a matter of fact, the efficient and scalable implementation of concurrent multiscale methods on clusters and supercomputers is a complicated endeavor. In this article we present the parallel multiscale simulation tool MACI which has been designed for efficient coupling between molecular dynamics and finite element codes. We propose a specification for a thin yet versatile interface for the coupling of molecular dynamics and finite element codes in a modular fashion. Further we discuss the parallelization strategy pursued in MACI, in particular, focusing on the parallel assembly of transfer operators and their efficient execution. T3 - ZIB-Report - 13-50 KW - Parallel KW - Atomistic to Continuum KW - Multiscale KW - MACI KW - Meshfree Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42354 SN - 1438-0064 ER - TY - GEN A1 - Hartmann, Carsten A1 - Banisch, Ralf A1 - Sarich, Marco A1 - Badowski, Thomas A1 - Schütte, Christof T1 - Characterization of Rare Events in Molecular Dynamics N2 - A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski's equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically) giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods. T3 - ZIB-Report - 13-51 KW - rare events KW - moleculare dynamics KW - optimal pathways KW - stochastic control KW - dynamic programming KW - change of measure KW - cumulant generating function Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42410 SN - 1438-0064 ER - TY - GEN A1 - Sarich, Marco A1 - Banisch, Ralf A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Markov State Models for Rare Events in Molecular Dynamics N2 - Rare but important transition events between long lived states are a key feature of many molecular systems. In many cases the computation of rare event statistics by direct molecular dynamics (MD) simulations is infeasible even on the most powerful computers because of the immensely long simulation timescales needed. Recently a technique for spatial discretization of the molecular state space designed to help overcome such problems, so-called Markov State Models (MSMs), has attracted a lot of attention. We review the theoretical background and algorithmic realization of MSMs and illustrate their use by some numerical examples. Furthermore we introduce a novel approach to using MSMs for the efficient solution of optimal control problems that appear in applications where one desires to optimize molecular properties by means of external controls. T3 - ZIB-Report - 13-52 KW - rare events KW - Markov state models KW - long timescales KW - optimal control Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42420 SN - 1438-0064 ER - TY - GEN A1 - Schütte, Christof A1 - Nielsen, Adam A1 - Weber, Marcus T1 - Markov State Models and Molecular Alchemy N2 - In recent years Markov State Models (MSMs) have attracted a consid- erable amount of attention with regard to modelling conformation changes and associated function of biomolecular systems. They have been used successfully, e.g., for peptides including time-resolved spectroscopic ex- periments, protein function and protein folding , DNA and RNA, and ligand-receptor interaction in drug design and more complicated multi- valent scenarios. In this article a novel reweighting scheme is introduced that allows to construct an MSM for certain molecular system out of an MSM for a similar system. This permits studying how molecular proper- ties on long timescales differ between similar molecular systems without performing full molecular dynamics simulations for each system under con- sideration. The performance of the reweighting scheme is illustrated for simple test cases including one where the main wells of the respective en- ergy landscapes are located differently and an alchemical transformation of butane to pentane where the dimension of the state space is changed. T3 - ZIB-Report - 14-05 KW - Girsanov Theorem KW - Stochastic Differential Equation KW - Importance Sampling Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-46718 SN - 1438-0064 ER -