MOLKERN: A library of software components for molecular modeling programs

Fomin, E. S.; Alemasov, N. A.; Chirtsov, A. S.; Fomin, A. E.

doi:10.1134/s0006350906070219

Cited by 6 publications

(4 citation statements)

References 5 publications

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“…The VT and LC methods with various modifications were implemented in the MOLKERN simulation software 30. Three implementations were developed for each method: (1) sequential C++ code, (2) vectorized C++ code, and (3) multithreaded vectorized C++ code.…”

Section: Implementation Of the Methodsmentioning

confidence: 99%

Consideration of data load time on modern processors for the Verlet table and linked‐cell algorithms

Fomin¹

2011

J Comput Chem

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Neighbor search algorithms are widely used in molecular dynamics for the direct computation of short-range pairwise interatomic potentials. These algorithms are based on the Verlet table (VT) and linked-cell (LC) methods. It is widely believed that the VT is more efficient than the LC. The analysis of these methods shows that in case when the average number of interactions per particle is relatively large, or more specifically, the particle density ρ and skin radius r(skin) meet the condition (4π/6)ρr (skin)3/27 ≫ 1, which may be true for most simulations of liquids, the number of memory data load operations in the LC is much less than that in the VT. Because memory access on modern processors is a bottleneck, this advantage of the LC should be and was in fact used, and a code outperforming the VT by a factor of almost 2 was obtained. Some modifications of the VT were proposed to reduce its disadvantage concerning memory data loading. The key modifications included automated skin radius tuning during simulations and compression of the VT to minimize duplications of atom identifiers in its nearby rows. Although these modifications had improved the performance, the VT failed to regain the superiority over the LC. The methods were tested in the MOLKERN simulation software by using SIMD and multithreading.

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Section: Implementation Of the Methodsmentioning

confidence: 99%

Consideration of data load time on modern processors for the Verlet table and linked‐cell algorithms

Fomin¹

2011

J Comput Chem

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“…Alexander Fedorov: You are right, today the perception of Soviet "shelf" cinema has become different, and this is clearly evident in the books and articles of Russian film historians of the 21st century (O. Kovalov, E. Margolit, A. Shpagin, V. Fomin, etc.). In my book I cite the opinions of many Russian film historians (Fomin, 1992, Fomin et al, 2012Margolit, 2012, etc. ), for whom banned Soviet films became the subject of a multifactorial study.…”

Section: Alexander Fedorovmentioning

confidence: 99%

Forbidden Soviet Cinema (1951-1991): A View from the 21st сentury

2021

International Journal of Media and Information Literacy

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In 2021 the Publishing House SM "Information for All" published a book by Professor Alexander Fedorov "Record holders of the banned Soviet cinema in the mirror of film criticism and viewers' opinions" (Fedorov, 2021). In this interview with Professor Marina Tselykh, Alexander Fedorov discussed the reasons for which films were banned, shelved or interrupted at various stages of their production in the USSR, how audiences reacted to the release of such "shelf" films during "perestroika," and other aspects of the topic.After reading this book it becomes clear how difficult was the fate of Soviet film directors, screenwriters and actors. The lives of some of the most talented filmmakers were ruined... For example, Alexander Askoldov was banned from working in the film industry for twenty years after his film "Commissar" was shot. And Soviet many films have been banned from cinemas and television or stopped while they were still in the making. And this despite the fact that many of them had real artistic value, were masterfully filmed.

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“…29 The monatomic gas argon was chosen as a test object. The reason for the choice was that the test of the algorithm and the e®ect of SIMDization in a monatomic system are more explicit.…”

Section: E®ect Of Sorting Typementioning

confidence: 99%

Interaction sorting method for molecular dynamics on multi-core SIMD CPU architecture

Matvienko

Alemasov

Fomin

2015

J. Bioinform. Comput. Biol.

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Molecular dynamics (MD) is widely used in computational biology for studying binding mechanisms of molecules, molecular transport, conformational transitions, protein folding, etc. The method is computationally expensive; thus, the demand for the development of novel, much more efficient algorithms is still high. Therefore, the new algorithm designed in 2007 and called interaction sorting (IS) clearly attracted interest, as it outperformed the most efficient MD algorithms. In this work, a new IS modification is proposed which allows the algorithm to utilize SIMD processor instructions. This paper shows that the improvement provides an additional gain in performance, 9% to 45% in comparison to the original IS method.

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MOLKERN: A library of software components for molecular modeling programs

Cited by 6 publications

References 5 publications

Consideration of data load time on modern processors for the Verlet table and linked‐cell algorithms

Consideration of data load time on modern processors for the Verlet table and linked‐cell algorithms

Forbidden Soviet Cinema (1951-1991): A View from the 21st сentury

Interaction sorting method for molecular dynamics on multi-core SIMD CPU architecture

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