Method for accurately calculating absolute free energy of gas molecules

A technology for accurate calculation of gas molecules, applied in the field of molecular dynamics simulation, which can solve problems such as difficulty in achieving absolute free energy

Pending Publication Date: 2021-01-08
SHENZHEN JINGTAI TECH CO LTD
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

Therefore, it is more difficult to accurately calculate the absolute free energy of liquid molecules

Method used

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  • Method for accurately calculating absolute free energy of gas molecules
  • Method for accurately calculating absolute free energy of gas molecules
  • Method for accurately calculating absolute free energy of gas molecules

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Embodiment Construction

[0043] The following will clearly and completely describe the technical solutions in the embodiments of the present invention with reference to the accompanying drawings in the embodiments of the present invention. Obviously, the described embodiments are only some, not all, embodiments of the present invention. Based on the embodiments of the present invention, all other embodiments obtained by persons of ordinary skill in the art without making creative efforts belong to the protection scope of the present invention.

[0044] In this embodiment, the calculation steps of the absolute free energy of butane (butane) molecules are as follows: figure 1 The butane structure shown is:

[0045] (1) Prepare the coordinate (pdb) file of the butane molecule, and use antechamber to capture the corresponding GAFF2 force field parameters;

[0046] (2) Call the yoda program, load the molecular coordinates and force field, and search for all flexible dihedral angles in the molecule;

[00...

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Abstract

The invention discloses a method for accurately calculating absolute free energy of gas molecules. The method comprises the following steps: S1, reducing an energy barrier of a flexible dihedral anglepotential energy surface in the gas molecules; and S2, calculating the absolute free energy of the gas molecules. According to the invention, automatic identification and potential energy surface scanning of a flexible dihedral angle in a molecule are realized, fitting of a dihedral angle potential energy surface is realized, dihedral angle parameters are automatically modified to reduce the potential energy surface to a specific value, a new WHAM program is realized, actual free energy can be obtained from potential energy reweight of biased and unbiased, and a set of feasible calculation process is designed. Gentle change of potential energy is realized when various types of energy are gradually removed from gas molecules; and all the processes are connected together, and automatic calculation of the absolute free energy of the gas molecules is achieved.

Description

technical field [0001] The invention belongs to the technical field of molecular dynamics simulation, in particular to a method for accurately calculating the absolute free energy of gas molecules. Background technique [0002] In recent years, the application of molecular simulation technology has become more and more extensive, and the demand for free energy calculation has also increased. At present, due to the stability of the crystal structure and the relatively small sampling space, there are some methods that can accurately predict the absolute free energy of solid molecules, which can be applied to the prediction and screening of stable experimental crystal forms of drug molecules. [0003] For the absolute free energy of liquid and gas molecules, there is no good and accurate prediction method. This makes it difficult to predict the properties of solid-liquid (such as melting point, solubility), solid-gas (such as sublimation enthalpy) and so on. [0004] There is...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F30/28G06F113/08G06F119/14
CPCG06F30/28G06F2113/08G06F2119/14
Inventor 彭春望马健温书豪杨明俊孙广旭赖力鹏
Owner SHENZHEN JINGTAI TECH CO LTD
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