Atomic type definition system and atomic type matching method thereof

Abstract

The invention belongs to the technical field of force fields and particularly discloses an atomic type definition system and an atomic type matching method. The system comprises an atomic type visualization UI, an atomic type matching module, an atomic type data management module and an atomic type format conversion module, wherein the atomic type data management module comprises an atomic type definition data packet. Through the designed atomic type definition mode, a nesting relation, an inheriting relation, a hierarchical relation, a tree relation and various complicated atomic chemical environments can be described, description capability is improved, richer and more precise atomic types can be described, and force field calculation can be more accurate; convenient operation can be performed on atomic types, and addition, deletion, modification, finding and multidimensional statistical analysis are all quite visual and convenient; and compared with existing methods, efficiency is higher, and matching accuracy is higher.

Description

technical field [0001] The invention belongs to the field of force field technology, and specifically relates to an atom type definition system and an atom type matching method. Background technique [0002] Force field techniques are computational techniques used in molecular and crystal simulations to accurately calculate structures and energies. The atom type definition system is the core system in the force field technology. Existing force fields including Amber, Charmm, OPLS, OpenFF, etc. have their own atom type definition systems, and the number of the respective atom types, the chemical environment around the atom The definition method, data format and usage method are all different. The pros and cons of the atom type definition system will not only affect the difficulty and cost of force field construction, but also directly affect the calculation accuracy of the force field during use. [0003] The main problems of the existing force field atom type definition sy...

AI Technical Summary

Problems solved by technology

[0004] 1. The atom type does not distinguish enough about the chemical environment around the atom, and many different types of atoms are classified as the same type, resulting in a decrease in calculation accuracy;

[0005] 2. The definition method of the atom type has great limitations. Generally, the definition method based on SMARTS and wildcards is relatively large when describing the chemical environment such as rings, bridges, and nesting, and the performance is not good;

[0006] 3. The atomic type is not easy to expand. When it is found that the atomic type is not enough, there is no perfect method and tool expansion when new types are needed, resulting in the consumption of a lot of manpower and time costs for each upgrade. Generally, it takes 2 to 3 years in the shortest period, and in the long term. 5 to 10 years;

[0007] 4. It is difficult to view and edit atomic types without the assistance of friendly visualization tools, which makes it easy to make mistakes when viewing and modifying

[0008] 5. It is difficult to convert formats between each other. Each is based on the data model of text lines for storage and use. It is very difficult when users want to cross-use or compare each other

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