A Test Set for Molecular Dynamics Algorithms
This article describes a collection of model problems for aiding numerical analysts, code developers and others in the design of computational methods for molecular dynamics (MD) simulation. Common types of calculations and desirable features of algorithm
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Abstract. This article describes a collection of model problems for aid ing numerical analysts, code develop ers and others in t he design of computat ional methods for molecul ar dyn amics (MD) simulation . Common ty pes of calculations and desirable features of algorit hms are surveyed , and these are used to guide selection of representative mod els. By including essential features of certain classes of mol ecul ar systems, but ot he rwise limiting the ph ysical and qu antit ative details, it is hoped t hat the t est set ca n help to fa cilit at e cross -disci plinary algorit hm and code development efforts.
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Introduction and Background
Over the past two decad es, computational scientists have turned increasing attent ion to the field of molecular modeling. Important advances have been mad e in t he design of efficient algorit hms for problems such as fast summation methods for comput ing non-bonded at omic int er actions [1,2]' long-time numer ical integr ation of equat ions of motion[3-5], non-N ewtonian dynami cal formul ations for simulat ion in a variety of stat ist ical mechanic al ensembles [6- 8], and optimization. These proj ects have often involved mathem atician s and/or compute r scient ists who , though adept at algorit hm and software development , may possess limit ed or no physic al and chemical knowledge. An important ste p in the developm ent of a computat ional method is t esting on model problems which possess cha racterist ic properties yet are as simple as possible so that numerical experiment s are not too time consuming. The purpose is generally to assess the performan ce of a particular method in connect ion with certain t ar get ed mod el features. As increasin gly complex computat iona l approaches appear in the liter ature, it is becoming evident that the choice of proper t est systems can great ly ease code compa risons and algorit hm development. Compilations of t est problems have become well established in other fields, for example in opt imizat ion [9- 11] and differential equa t ions [12,13]. The CASP project [14] (Cri ti cal Assessment of t echniques for protein Structure Predicti on) prov ides a t estbed for obj ective t esting and comparison of methods for identifying protein st ruct ure from sequence . To our knowledge, T. Schlick et al. (eds.), Computational Methods for Macromolecules: Challenges and Applications © Springer-Verlag Berlin Heidelberg 2002
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Bart h, Leim kuhler , Reich
no simil ar collect ion exists for design and evaluat ion of molecular dyn am ics methods. We have assembled here a few elementary mod els dr awn primarily from the molecular simulat ion liter ature. Our goal is t o provide adequate det ail so t hat an applied mathematician , with little access t o MD codes and virtually no chemical/physical und erst anding, could- base d only t his pap er-perform simulat ions that rese mble, in relevant ways, t he mor e complex problems of curre nt research int erest. Our first step is t o int roduce a basic vocabulary for molecul ar dyn ami c
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