Implementing efficient concerted rotations using Mathematica and C code

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Authors	TUBIANA L. JURÁSEK Miroslav COLUZZA I.
Year of publication	2018
Type	Article in Periodical
Magazine / Source	EUROPEAN PHYSICAL JOURNAL E
MU Faculty or unit	Central European Institute of Technology
Citation
Doi	http://dx.doi.org/10.1140/epje/i2018-11694-7
Keywords	INTRINSICALLY UNSTRUCTURED PROTEINS; MONTE-CARLO SIMULATIONS; COARSE-GRAINED MODELS; MOLECULAR-DYNAMICS; SYSTEMS; ALGORITHM
Attached files	Tubiana2018_Article_ImplementingEfficientConcerted.pdf
Description	In this article we demonstrate a general and efficient metaprogramming implementation of concerted rotations using Mathematica. Concerted rotations allow the movement of a fixed portion of a polymer backbone with fixed bending angles, like a protein, while maintaining the correct geometry of the backbone and the initial and final points of the portion fixed. Our implementation uses Mathematica to generate a C code which is then wrapped in a library by a Python script. The user can modify the Mathematica notebook to generate a set of concerted rotations suited for a particular backbone geometry, without having to write the C code himself. The resulting code is highly optimized, performing on the order of thousands of operations per second.
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