Calculation method for macromolecule dihedral angle interaction forces

A calculation method and dihedral angle technology, applied in the field of molecular dynamics, can solve problems such as difficult control of calculation errors, unintuitive expression, and difficulty in implementation

Inactive Publication Date: 2013-04-24
HOHAI UNIV
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0003] Traditionally, the calculation of this problem adopts the Cartesian coordinate method, that is, the four points are expressed as three-dimensional Cartesian coordinates, and the four forces are also expressed as three-dimensional Cartesian coor...

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  • Calculation method for macromolecule dihedral angle interaction forces
  • Calculation method for macromolecule dihedral angle interaction forces
  • Calculation method for macromolecule dihedral angle interaction forces

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Embodiment Construction

[0067] Below in conjunction with accompanying drawing and specific embodiment, further illustrate the present invention, should be understood that these embodiments are only for illustrating the present invention and are not intended to limit the scope of the present invention, after having read the present invention, those skilled in the art will understand various aspects of the present invention Modifications in equivalent forms all fall within the scope defined by the appended claims of this application.

[0068]The invention provides the principle and calculation process of a calculation method for the interaction force of a four-point dihedral angle structure in a full vector format. It mainly includes the following two parts:

[0069] 1. The calculation principle of the full vector format;

[0070] 2. Realize the calculation flow of the algorithm.

[0071] Described below respectively.

[0072] 1 Calculation principle of full vector format

[0073] 1.1 The energy of...

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Abstract

The invention discloses a calculation method for macromolecule dihedral angle interaction forces for calculating interaction forces of four-point dihedral angle structures. The method comprises that positions of four atoms in three-dimensional space are expressed to be four direction vectors; four four-inner-product directional derivative vectors, eight three-point included angle directional derivative vectors and four double-tangent directional derivative vectors are calculated successively; four dihedral angle directional derivative vectors, an energy scalar derivative and the like are calculated; and vectors of four forces are calculated, and the calculation is completed. According to the calculation method, the data structure is simple, the calculation process is clear, and calculation errors are easy to control.

Description

technical field [0001] The invention belongs to the technical field of molecular dynamics, relates to a method for calculating the interaction force of a four-point dihedral structure with general significance in the field of molecular dynamics of biological macromolecules (DNA, protein, etc.), specifically a full vector Format calculation method. Background technique [0002] In the calculation of biological macromolecules, the calculation of the interaction force of the four-point dihedral structure is often encountered, such as figure 1 As shown, the four points i, j, k, and l in the figure are four atoms connected together by covalent bonds in three-dimensional space, forming a space dihedral angle structure, and the value of this dihedral angle is It is determined by the positions of the four atoms i, j, k, and l in three-dimensional space. and θ ijk is the angle between the planes of the three atoms i, j, k, θ jkl is the angle between the planes of the three atoms...

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Application Information

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IPC IPC(8): G06F19/10
Inventor 孟朝晖
Owner HOHAI UNIV
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