Automatic efficient DFTB repulsive potential fitting method

A repulsive potential and high-efficiency technology, applied in the field of bioinformatics, can solve problems such as slow development speed, repeated iterations, fitting repulsive potential compatibility and matching problems, and achieve the effect of solving compatibility problems

Active Publication Date: 2018-11-02
SHENZHEN JINGTAI TECH CO LTD
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  • Application Information

AI Technical Summary

Problems solved by technology

[0003] The current DFTB parameterization scheme establishes the training set manually and uses a large number of training sample points for spline curve fitting to determine the repulsion potential curve. Since the same repulsion potential needs to describe multiple bonding forms of two atom pairs, if Using a large number of training sample points for fitting can easily lead to the inability to accurately cover different bonding forms. For example, C...O interaction has two bonding modes of C-O/C=O, and the equilibrium positions are obviously different. Direct spline Fitting is difficult to balance two bond lengths
[0004] The spline fitting method can only fit one atom pair curve at a time, and the fitting sequence ha...

Method used

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  • Automatic efficient DFTB repulsive potential fitting method
  • Automatic efficient DFTB repulsive potential fitting method
  • Automatic efficient DFTB repulsive potential fitting method

Examples

Experimental program
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Effect test

Embodiment 1

[0037] Such as figure 1 As shown, a repulsive potential energy fitting method based on differential evolution algorithm includes the following steps:

[0038] Step (1): According to the target atom pair, generate a hydrogen-saturated molecular system according to the information of the atom itself, and use the B3LYP / cc-pVTZ method in Gaussian09 to optimize the molecular pair; according to the repulsion potential range, use the B3LYP / cc-pVTZ method Perform a spacing scan on atom pairs;

[0039] Step (2): use the G3B3 method in Gaussian09 to carry out high-precision energy calculation to the spacing scan;

[0040] Step (3): use the energy differential calculation force and the second derivative of energy obtained by the G3B3 method;

[0041] Step (4): the energy calculated by the structure, the G3B3 method, the second derivative of force and energy are stored in the database;

[0042] Step (5): Use DFTB+ and other programs that can perform DFTB calculations to obtain the ene...

Embodiment 2

[0070] Since the fitting process focuses on using the equilibrium position, energy and force of different bond types, only a few sample points are used to assist the fitting, and the information of the equilibrium position is mainly reserved, and the weights are approximately equal, which overcomes the problem of unbalanced fitting of bond types ; For example: C—O needs to fit the repulsive energy in the interval from 2.0 to 4.6 Bohr. According to the uniform discrete interval of 0.05, at least 52 training samples are required. As before figure 2 As shown, the parameters related to the repulsion potential at the equilibrium position are small, and the parameters at the starting point are large, causing the fitting weight to decrease from the starting point to the end point. The fitting result tends to obtain a closer equilibrium position; The bond type with larger relative parameters is correspondingly more reliable. Among C-O, the C=O bond will be described more accurately. F...

Embodiment 3

[0073] Due to the fitting method of linear equations used, the fitting of multiple repulsive potentials can be put into one equation at ordinary times, so as to realize the fitting of multiple repulsive potentials and solve the problem of parameter compatibility; for example, for the sample of C-O To fit the strips, you must first prepare all the parameters of H-H, C-C, O-O, O-H, and C-H; if any parameters are missing, you must prepare the corresponding parameters before continuing. Moreover, there are coupling compatibility problems between the parameters. For example, H-H The interaction between them will cause the calculation of C-O training sample values ​​and affect the fitting of C-O. To obtain compatible parameters, multiple sets of parameters must be adjusted repeatedly to determine the final repulsion potential parameters, which is inefficient; this method uses linear equations For fitting, the parameters of H-H and C-O can be put into a linear equation system for solu...

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Abstract

The invention provides an automatic efficient DFTB repulsive potential fitting method. The method comprises the following steps: step (1) optimizing molecule containing atom pair; performing atom pairspacing scanning according to a repulsive potential effect interval; step (2) performing high-precision energy calculation on a scanning result; step (3) energy different calculation power and energysecond derivative; step (4) saving the structure, the energy, the power and the energy second derivative in a database; step (5) obtaining the energy not containing the repulsive potential, the power, and the energy second derivative so as to obtain a repulsive potential target value; step (6) converting the separated repulsive potential target value into a spline curve; step (7) splicing multiple spline curves at an average location between the balance location points to obtain brand new training data; step (8) constructing a training set by using a unnecessary sample and a selection sample;and step (9) decomposing the fitting repulsive potential by using a singular value. The key type imbalance fitting problem is overcome.

Description

technical field [0001] The invention belongs to biological information technology and relates to the design of functional materials, in particular to an automatic and efficient DFTB repulsion potential fitting method. Background technique [0002] DFTB is a high-precision quantum chemical method with fast calculation, which achieves an effective balance between calculation scale and precision, and has a wide range of applications in the fields of biological protein simulation and functional material design. Repulsion potential is an important part of DFTB parameters, and its reliability seriously affects the accuracy of calculation and simulation. [0003] The current DFTB parameterization scheme establishes the training set manually and uses a large number of training sample points for spline curve fitting to determine the repulsion potential curve. Since the same repulsion potential needs to describe multiple bonding forms of two atom pairs, if Using a large number of tra...

Claims

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Application Information

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IPC IPC(8): G06F19/16G06F19/28
Inventor 曾群张佩宇金颖滴马健赖力鹏温书豪
Owner SHENZHEN JINGTAI TECH CO LTD
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