A processing method and device for constructing a polarization force field model
By providing configuration optimization methods and polarization models, the problems of poor molecular structure rationality and mismatch of force field potential functions in the construction process of polarization force field model in the prior art are solved, and a more efficient and accurate construction of polarization force field model is achieved.
Patent Information
- Application Number
- CN202410026963.2
- Authority / Receiving Office
- CN · China
- Patent Type
- Patents(China)
- Current Assignee / Owner
- Filing Date
- 2024-01-08
- Publication Date
- 2025-06-17
- Estimated Expiration
- 2044-01-08
AI Technical Summary
When building polarized force field models, the existing technology lacks effective pretreatment tools, resulting in poor molecular structure rationality and frequent mismatch of force field potential functions, which affects the accuracy and efficiency of simulation.
A processing method is provided. By giving four configuration optimization methods (Hartree-Fock, density functional, perturbation theory and coupling cluster method) and three polarization models (fluctuation and fall charge model, Drude oscillator model and induced dipole model), the molecular system to be processed is optimized and polarization force field potential function is constructed to generate the optimized force field parameter set to form the corresponding polarization force field model.
It improves the rationality of the molecular architecture, enhances the matching richness and configuration accuracy of the polarization force field model, gets rid of manpower limitations, and improves processing efficiency.
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Figure CN117831644B_ABST
Abstract
Description
Technical Field
[0001] The present invention relates to the technical field of data processing, and particularly relates to a processing method and device for constructing a polarization force field model. Background Art
[0002] The implementation steps of molecular dynamics simulation are generally divided into a preprocessing stage and a simulation stage. The preprocessing stage is responsible for selecting the molecular force field type and generating the corresponding molecular force field model, and the simulation stage is responsible for constructing the motion equation based on the molecular force field model and implementing the simulation based on the constructed equation. Among them, the molecular force field model includes the corresponding molecular system, force field potential function, and force field parameter set. Here, the force field parameter set is actually a set of variables of the force field potential function related to the structure of the molecular system to be simulated. The polarization force field is a type of molecular force field. At present, the tools for implementing simulation on the market are all relatively powerful and can also be compatible with molecular force field models in different file formats. However, the tools for performing preprocessing work are relatively scarce. In most cases, developers need to use some basic editing tools to perform preprocessing on the molecular system to be simulated in a fully manual / semi-manual manner. On the one hand, this processing method has relatively low work efficiency and the rationality of the output molecular structure is also poor. The low rationality of the molecular structure will affect the simulation efficiency in the subsequent simulation stage. On the other hand, the problem of force field potential function mismatch is also likely to occur. An error in the force field potential function or a misconfiguration of the force field parameter set will directly affect the simulation accuracy in the subsequent simulation stage. Summary of the Invention
[0003] The object of the present invention is to provide a processing method, device, electronic device and computer-readable storage medium for constructing a polarization force field model in view of the defects of the prior art. The present invention provides four configuration optimization methods for selection: Hartree-Fock (hereinafter referred to as HF) method, density functional theory (DFT) method, perturbation theory method (hereinafter referred to as MPn method), and coupled cluster method, and provides three polarization models for selection: Fluctuating Charge Model, Drude Oscillator Model, and Induced Point Dipoles model; and perform configuration optimization on the molecular system to be processed based on the selected configuration optimization method, and construct the polarization force field potential function based on the selected polarization model; and construct the force field parameter set based on the optimized molecular system and the polarization force field potential function of the specified model, and the optimized molecular system, the force field potential function and the force field parameter set obtained form the corresponding polarization force field model for output. Through the present invention, on the one hand, the structural rationality of the molecular system can be improved based on configuration optimization, on the other hand, the configuration richness and configuration accuracy of the polarization force field model can be improved through the standard processing flow of the three polarization models, and on the third hand, the processing efficiency can be improved by getting rid of human limitations.
[0004] To achieve the above object, a first aspect of an embodiment of the present invention provides a processing method for constructing a polarization force field model, the method comprising:
[0005] Receiving a molecular system, a configuration optimization method option, and a polarization model option as a corresponding first molecular system, a first option, and a second option; the first molecular system includes a plurality of first molecules and a plurality of first connection bonds; the first molecule includes a plurality of first atoms; the particle attributes of the first atom include atomic element type, atomic mass, atomic position coordinates, and atomic charge number; the first connection bond is used to connect two of the first atoms; the bond attributes of the first connection bond include connection bond type; the first option includes Hartree-Fock method, density functional method, perturbation theory method, and coupled cluster method; the second option includes Fluctuating Charge Model, Drude Oscillator Model, and Induced Point Dipoles model;
[0006] Performing structural optimization processing on the first molecular system based on the first option;
[0007] Constructing a polarization force field potential function according to the second option to obtain a corresponding first potential function and a first force field parameter set; and forming a corresponding first molecular system polarization force field model from the first molecular system, the first potential function, and the first force field parameter set.
[0008] Preferably, the structural optimization process of the first molecular system based on the first option specifically includes:
[0009] When the first option is the Hartree-Fock method, the structural optimization of the first molecular system is performed based on HF / 2-ZETA, HF / 3-ZETA, or HF / 4-ZETA calculations;
[0010] When the first option is the density functional method, the structural optimization of the first molecular system is performed based on B3LYP / 2-ZETA, B3LYP / 3-ZETA, or B3LYP / 4-ZETA calculations;
[0011] When the first option is the perturbation theory method, the structural optimization of the first molecular system is performed based on MP2 / 2-ZETA, MP2 / 3-ZETA, or MP2 / 4-ZETA calculations;
[0012] When the first option is the coupled cluster method, the structural optimization of the first molecular system is performed based on CCSD(T) / 2-ZETA or CCSD(T) / 3-ZETA calculations.
[0013] Preferably, the construction of the polarization force field potential function according to the second option to obtain the corresponding first potential function and the first set of force field parameters specifically includes:
[0014] Set the total potential function U tot = U bon + U ang + U tor + U vdW + U ele ; where U bon is the bond stretching potential function, U ang is the bond angle bending potential function, U tor is the dihedral angle torsion potential function, U vdW is the van der Waals potential function, U ele is the electrostatic potential function;
[0015] When the second option is the fluctuating charge model, the electrostatic potential function U tot of the total potential function U ele is corrected to obtain the corresponding first potential function and the first set of force field parameters;
[0016] When the second option is the Drude oscillator model, a Drude harmonic oscillator is added to the first molecular system to obtain a new first molecular system; and by adding a harmonic oscillator vibration potential function U tot to the total potential function U har-dAnd correct the electrostatic potential function U ele to obtain the corresponding first potential function and the first set of force field parameters;
[0017] When the second option is the induced dipole model, add the induced dipole potential function U tot to the total potential function U pol to obtain the corresponding first potential function and the first set of force field parameters.
[0018] Furthermore, the bond stretching potential function U bon is:
[0019]
[0020] where 1 ≤ i ≤ B, A is the total number of the first connecting bonds; u b,i is the bond stretching potential function of any one of the first connecting bonds; k b,i is the bond stretching force constant of the corresponding first connecting bond; the standard bond length l 0,i is the bond length value of the corresponding first connecting bond in the equilibrium state; the bond length variable l i is the variable bond length value of the corresponding first connecting bond;
[0021] The bond angle bending potential function U ang is:
[0022]
[0023] where 1 ≤ j ≤ B, B is the total number of the first bond angles, and the first bond angle is the angle between two of the first connecting bonds composed of three sequentially connected first atoms; u a,j is the bond angle bending potential function of any one of the first bond angles; k θ,j is the bond angle bending force constant of the corresponding first bond angle; the standard bond angle θ 0,j is the angle value of the corresponding first bond angle in the equilibrium state, and the bond angle variable θ j is the variable angle value of the corresponding first bond angle;
[0024] The dihedral angle torsion potential function U tor is:
[0025]
[0026] where 1 ≤ m ≤ C, C is the total number of the first dihedral angles, and the first dihedral angle is the angle between two first intersecting planes formed by three of the first connecting bonds composed of four sequentially connected first atoms; u t,mis the dihedral angle torsional potential function of any one of the first dihedral angles; the constant n is the number of times the energy minimum appears when rotating 360° around the bond; V n,m is the dihedral angle torsional potential constant of the corresponding first dihedral angle; the standard dihedral angle ω 0,m is the angle value of the corresponding first dihedral angle in the equilibrium state, and the value of the standard dihedral angle ω 0,m includes 0 and π; the dihedral angle variable ω m is the variable angle value of the corresponding first dihedral angle;
[0027] The van der Waals potential function U vdW is:
[0028]
[0029] where 1 ≤ x ≤ N tom , 2 ≤ y ≤ N tom , N tom is the total number of the first atoms; u v,x,y is the van der Waals potential function between any pair of the first atoms; ε xy is the potential well depth of the corresponding atom pair; σ xy is the collision distance of the corresponding atom pair; r xy is the atomic spacing of the corresponding atom pair;
[0030] The electrostatic potential function U ele is:
[0031]
[0032] where u e,x,y is the electrostatic potential function between any pair of the first atoms; the atomic charge number q x is the atomic charge number of the x-th first atom, and the atomic charge number q y is the atomic charge number of the y-th first atom.
[0033] Further, the electrostatic potential function U tot of the total potential function U ele is corrected to obtain the corresponding first potential function and the first force field parameter set, specifically including:
[0034] The electrostatic potential function U tot of the total potential function U ele is corrected to:
[0035]
[0036] where the atomic charge variable Q x , Q yis the variable charge number of the two first atoms in the corresponding atom pair;
[0037] Take the new total potential function U tot as the corresponding first potential function; and from the bond stretching force constant k corresponding to all the first connecting bonds in the first molecular system b,i and the standard bond length l 0,i , the bond angle bending force constant k corresponding to all the first bond angles θ,j and the standard bond angle θ 0,j , the dihedral angle torsion potential constant V corresponding to all the first dihedral angles n,m and the standard dihedral angle ω 0,m , the potential well depth ε corresponding to all atom pairs xy and the collision distance σ xy to form the corresponding first force field parameter set.
[0038] Furthermore, adding Drude oscillators to the first molecular system to obtain the new first molecular system specifically includes:
[0039] Based on a preset oscillator addition rule, add a Drude oscillator connected to it to each of some or all of the first atoms in the first molecular system, denoted as the corresponding first oscillator; the particle attributes of the first oscillator include the paired atom identifier, the oscillator position coordinates, and the oscillator charge number; the atomic charge number of the first atom before adding the first oscillator is q0, the atomic charge number of the first atom before adding the first oscillator is q1, and the oscillator charge number of the corresponding first oscillator is q2, then the corresponding relationship between the three charge numbers should be: q2 = q0 - q1.
[0040] Furthermore, by adding the oscillator vibration potential function U tot to the total potential function U har -d and correcting the electrostatic potential function U ele to obtain the corresponding first potential function and the first force field parameter set, specifically including:
[0041] Set the oscillator vibration potential function U har-d as:
[0042]
[0043] where 1 ≤ o ≤ D, D is the total number of the first oscillators; u har-d,o is the oscillator vibration potential function of the first oscillator; k d,o is the force constant of the corresponding first oscillator; r ois the distance between the corresponding first harmonic oscillator and the corresponding first atom;
[0044] Add the harmonic oscillator vibration potential function U har-d to the total potential function U tot to obtain the new total potential function U tot which is: U tot = U bon + U ang + U tor + U vdw + U ele + U har-d ;
[0045] Modify the electrostatic potential function U tot of the new total potential function U ele to:
[0046]
[0047]
[0048] where 1 ≤ p ≤ D, 1 ≤ s ≤ N tom , 2 ≤ z ≤ N tom ; u e,o,p is the electrostatic potential function between any pair of the first harmonic oscillators; u e,o,s is the electrostatic potential function between any one of the first harmonic oscillators and any one of the first atoms; u e,s,z is the electrostatic potential function between any pair of the first atoms; the harmonic oscillator charge variable q o , q p are the variable charge numbers of the corresponding first harmonic oscillators; the atomic charge variables q s , q z are the variable charge numbers of the corresponding first atoms; r op is the distance between the corresponding two first harmonic oscillators; r os is the distance between the corresponding first harmonic oscillator and one of the first atoms; r sz is the distance between the corresponding two first atoms;
[0049] Take the new total potential function U tot as the corresponding first potential function; and from all the bond stretching force constants k b,i and the standard bond length l 0,i corresponding to all the first connecting bonds in the first molecular system, all the bond angle bending force constants k θ,j and the standard bond angle θ 0,j , all the dihedral angle torsion potential constants V n,mand the standard dihedral angle ω 0,m , the depth of the potential well ε corresponding to all atom pairs xy and the collision distance σ xy , the force constant k of all the first harmonic oscillators d,o constitute the corresponding set of the first force field parameters.
[0050] Furthermore, adding the induced dipole potential function U tot to the total potential function U pol to obtain the corresponding first potential function and the set of the first force field parameters, specifically including:
[0051] Set the induced dipole potential function U pol as:
[0052]
[0053]
[0054] where 1 ≤ f, g ≤ N tom , g ≠ f; taking each of the first atoms as an induced dipole point position, then u pol,f , u pol,g are the induced dipole potential functions of the corresponding f - th and g - th induced dipole point positions respectively; E 0,f is the induced electric field generated by the permanent charge of the first molecular system at the f - th induced dipole point position; α f is the polarizability tensor of the f - th induced dipole point position; T fg is the transformation matrix corresponding to the f - th and g - th induced dipole point positions; r fg is the distance between the f - th and g - th induced dipole point positions; I is the preset identity matrix; x, y, z are the three - dimensional rectangular coordinate components pointing from the f - th to the g - th induced dipole point position;
[0055] Adding the induced dipole potential function U pol to the total potential function U tot to obtain the new total potential function U tot as: U tot = U bon + U ang + U tor + U vdW + U ele + U pol ;
[0056] Taking the new total potential function U tot as the corresponding first potential function; and from the force constant k b,i of all the first connection bonds in the first molecular systemand the standard bond length l 0,i wherein, for all the first bond angles, the bond angle bending force constant k θ,j and the standard bond angle θ 0,j wherein, for all the first dihedral angles, the dihedral angle torsional potential constant V n,m and the standard dihedral angle ω 0,m wherein, for all atom pairs, the potential well depth ε xy and the collision distance σ xy wherein, for all the first atoms, the atomic charge number q, and for all the positions of the induced dipoles, the induced electric field E 0,f constitute the corresponding first set of force field parameters.
[0057] In a second aspect of the embodiments of the present invention, there is provided an apparatus for implementing the processing method for constructing a polarization force field model described in the first aspect above. The apparatus includes: a data receiving module, a configuration optimization module, and a model construction module;
[0058] The data receiving module is configured to receive a molecular system, configuration optimization method options, and polarization model options as a corresponding first molecular system, first options, and second options. The first molecular system includes a plurality of first molecules and a plurality of first connecting bonds. The first molecules include a plurality of first atoms. The particle attributes of the first atoms include atomic element type, atomic mass, atomic position coordinates, and atomic charge number. The first connecting bonds are used to connect two of the first atoms. The bond attributes of the first connecting bonds include bond type. The first options include Hartree - Fock method, density functional method, perturbation theory method, and coupled cluster method. The second options include fluctuating charge model, Drude oscillator model, and induced dipole model;
[0059] The configuration optimization module is configured to perform structural optimization processing on the first molecular system based on the first options;
[0060] The model construction module is configured to construct a polarization force field potential function according to the second options to obtain a corresponding first potential function and a first set of force field parameters; and form a corresponding first molecular system polarization force field model from the first molecular system, the first potential function, and the first set of force field parameters.
[0061] In a third aspect of the embodiments of the present invention, there is provided an electronic device, including: a memory, a processor, and a transceiver;
[0062] The processor is configured to be coupled with the memory, read and execute instructions in the memory to implement the method steps described in the first aspect above;
[0063] The transceiver is coupled to the processor, and the processor controls the transceiver to send and receive messages.
[0064] In a fourth aspect of the embodiments of the present invention, a computer-readable storage medium is provided. The computer-readable storage medium stores computer instructions. When the computer instructions are executed by a computer, the computer is caused to execute the instructions of the method described in the first aspect above.
[0065] The embodiments of the present invention provide a processing method, device, electronic device, and computer-readable storage medium for constructing a polarization force field model. The present invention provides four configuration optimization methods for selection: the Hartree-Fock method, the density functional method, the perturbation theory method, and the coupled cluster method, and provides three polarization models for selection: the fluctuating charge model, the Drude oscillator model, and the induced dipole model. And based on the configuration optimization method selected by the user, the molecular system to be processed is optimized in configuration, and the polarization force field potential function is constructed based on the polarization model selected by the user. And based on the optimized molecular system and the polarization force field potential function of the specified model, a force field parameter set is constructed, and the corresponding polarization force field model is output from the obtained optimized molecular system, force field potential function, and force field parameter set. Through the present invention, on the one hand, the rationality of the molecular system structure is improved based on configuration optimization, on the other hand, the configuration richness and configuration accuracy of the polarization force field model are improved through the standard processing flow of the three polarization models, and on the third hand, the human limitation is eliminated and the processing efficiency is improved. Description of the Drawings
[0066] Figure 1 It is a schematic diagram of a processing method for constructing a polarization force field model provided by Embodiment 1 of the present invention;
[0067] Figure 2 It is a module structure diagram of a processing device for constructing a polarization force field model provided by Embodiment 2 of the present invention;
[0068] Figure 3 It is a schematic diagram of the structure of an electronic device provided by Embodiment 3 of the present invention. Detailed Embodiments
[0069] In order to make the objectives, technical solutions, and advantages of the present invention clearer, the present invention will be further described in detail below with reference to the accompanying drawings. Obviously, the described embodiments are only a part of the embodiments of the present invention, rather than all of the embodiments. All other embodiments obtained by those of ordinary skill in the art based on the embodiments of the present invention without creative efforts shall fall within the protection scope of the present invention.
[0070] Embodiment 1 of the present invention provides a processing method for constructing a polarization force field model, as Figure 1As shown in the schematic diagram of a processing method for constructing a polarization force field model provided in the first embodiment of the present invention, the method mainly includes the following steps:
[0071] Step 1, receive a molecular system, a configuration optimization method option, and a polarization model option as the corresponding first molecular system, first option, and second option;
[0072] Among them, the first molecular system includes a plurality of first molecules and a plurality of first connection bonds; the first molecule includes a plurality of first atoms; the particle attributes of the first atom include atomic element type, atomic mass, atomic position coordinates, and atomic charge number; the first connection bond is used to connect two first atoms; the bond attributes of the first connection bond include connection bond type; the first option includes Hartree - Fock method, density functional method, perturbation theory method, and coupled cluster method; the second option includes fluctuating charge model, Drude oscillator model, and induced dipole model.
[0073] Here, the four configuration optimization methods provided in the embodiments of the present invention have different calculation accuracies and calculation amounts. Among them, the Hartree - Fock method has the coarsest calculation accuracy but the smallest calculation amount, and the coupled cluster method has the finest calculation accuracy but the largest calculation amount. The order from high to low in terms of calculation accuracy and calculation amount is coupled cluster method, perturbation theory method, density functional method, Hartree - Fock method. The user can select any one of them according to the computing power of their own device for subsequent configuration optimization processing. The three polarization models provided in the embodiments of the present invention basically cover the current mainstream polarization models, providing a relatively rich configuration selection for the user.
[0074] Step 2, perform structural optimization processing on the first molecular system based on the first option;
[0075] Specifically, it includes: Step 21, when the first option is the Hartree - Fock method, perform structural optimization on the first molecular system based on HF / 2 - ZETA, HF / 3 - ZETA, or HF / 4 - ZETA calculation;
[0076] Here, the HF / 2-ZETA, HF / 3-ZETA or HF / 4-ZETA calculations are quantum chemical calculation processes carried out using the Hartree-Fock method and implemented at the levels of 2-zeta basis sets represented by 6-31G, pVDZ, def2-DZVP, 3-zeta basis sets represented by 6-311G, pVTZ, def2-TZVP, or 4-zeta basis sets represented by pVQZ, def2-QZVP. This calculation process can perform single-point energy calculations for each site of the first molecular system to obtain the total single-point energy of the entire system. Then, by iteratively optimizing the first molecular system in the direction of minimizing the total single-point energy, a corresponding optimized structure can be obtained;
[0077] Step 22, when the first option is the density functional method, perform structure optimization on the first molecular system based on B3LYP / 2-ZETA, B3LYP / 3-ZETA or B3LYP / 4-ZETA calculations;
[0078] Here, the B3LYP / 2-ZETA, B3LYP / 3-ZETA or B3LYP / 4-ZETA calculations are quantum chemical calculation processes carried out using a DFT method (such as the B3LYP method, ωB97 series methods, Minnesota functional series methods, PBE series methods, etc.) and implemented at the levels of 2-zeta basis sets represented by 6-31G, pVDZ, def2-DZVP, 3-zeta basis sets represented by 6-311G, pVTZ, def2-TZVP, or 4-zeta basis sets represented by pVQZ, def2-QZVP. This calculation process can perform single-point energy calculations for each site of the first molecular system to obtain the total single-point energy of the entire system. Then, by iteratively optimizing the first molecular system in the direction of minimizing the total single-point energy, a corresponding optimized structure can be obtained;
[0079] Step 23, when the first option is the perturbation theory method, perform structure optimization on the first molecular system based on MP2 / 2-ZETA, MP2 / 3-ZETA or MP2 / 4-ZETA calculations;
[0080] Here, MP2 / 2-ZETA, MP2 / 3-ZETA, or MP2 / 4-ZETA calculations are quantum chemical calculation processes carried out using an MPn perturbation theory method and implemented respectively at the levels of 2-zeta basis sets represented by 6-31G, pVDZ, def2-DZVP, 3-zeta basis sets represented by 6-311G, pVTZ, def2-TZVP, and 4-zeta basis sets represented by pVQZ, def2-QZVP. This calculation process can perform single-point energy calculations for each site of the first molecular system to obtain the total single-point energy of the entire system. Then, by iteratively optimizing the first molecular system in the direction of minimizing the total single-point energy, a corresponding optimized structure can be obtained;
[0081] Step 24, when the first option is the coupled cluster method, perform structure optimization on the first molecular system based on CCSD(T) / 2-ZETA or CCSD(T) / 3-ZETA calculations.
[0082] Here, CCSD(T) / 2-ZETA or CCSD(T) / 3-ZETA calculations are quantum chemical calculation processes carried out using a coupled cluster method (CCSD(T) method) and implemented respectively at the levels of 2-zeta basis sets represented by 6-31G, pVDZ, def2-DZVP or 3-zeta basis sets represented by 6-311G, pVTZ, def2-TZVP. This calculation process can perform single-point energy calculations for each site of the first molecular system to obtain the total single-point energy of the entire system. Then, by iteratively optimizing the first molecular system in the direction of minimizing the total single-point energy, a corresponding optimized structure can be obtained.
[0083] Step 3, construct a polarizable force field potential function according to the second option to obtain a corresponding first potential function and a first set of force field parameters; and form a corresponding polarizable force field model of the first molecular system from the first molecular system, the first potential function, and the first set of force field parameters;
[0084] Specifically, it includes: Step 31, construct a polarizable force field potential function according to the second option to obtain a corresponding first potential function and a first set of force field parameters;
[0085] Specifically, it includes: Step 311, set the total potential function as:
[0086] U tot =U bon +U ang +U tor +U vdw +U ele ;
[0087] Here, the total potential function U tot is a classical force field potential function. In the function: Ubon is the bond stretching potential function, U ang is the bond angle bending potential function, U tor is the dihedral angle torsion potential function, U vdW is the van der Waals potential function, U ele is the electrostatic potential function;
[0088] Among them:
[0089] 1) The bond stretching potential function U bon is:
[0090]
[0091] Here, 1 ≤ i ≤ B, A is the total number of the first connecting bonds; u b,i is the bond stretching potential function of any one of the first connecting bonds; k b,i is the bond stretching force constant of the corresponding first connecting bond; the standard bond length l 0,i is the bond length value of the corresponding first connecting bond in the equilibrium state; the bond length variable l i is the variable bond length value of the corresponding first connecting bond;
[0092] 2) The bond angle bending potential function U ang is:
[0093]
[0094] Here, 1 ≤ j ≤ B, B is the total number of the first bond angles, and the first bond angle is the angle between two first connecting bonds composed of three sequentially connected first atoms; u a,j is the bond angle bending potential function of any one of the first bond angles; k θ,j is the bond angle bending force constant of the corresponding first bond angle; the standard bond angle θ 0,j is the angle value of the corresponding first bond angle in the equilibrium state, and the bond angle variable θ j is the variable angle value of the corresponding first bond angle;
[0095] 3) The dihedral angle torsion potential function U tor is:
[0096]
[0097] Here, 1 ≤ m ≤ C, C is the total number of the first dihedral angles, and the first dihedral angle is the angle between two first intersecting planes formed by three first connecting bonds composed of four sequentially connected first atoms; u t,m is the dihedral angle torsion potential function of any one of the first dihedral angles; the constant n is the number of times of the energy minimum when rotating 360° around the bond; V n,m is the dihedral angle torsion potential constant of the corresponding first dihedral angle; the standard dihedral angle ω 0,mis the angular value of the corresponding first and second dihedral angles in the equilibrium state, and the standard dihedral angle ω 0,m takes values including 0 and π; the dihedral angle variable ω m is the variable angular value of the corresponding first and second dihedral angles;
[0098] 4) The van der Waals potential function U vdW is:
[0099]
[0100] Here, 1 ≤ x ≤ N tom , 2 ≤ y ≤ N tom , N tom is the total number of the first atoms; u v,x,y is the van der Waals potential function between any pair of the first atoms; ε xy is the potential well depth of the corresponding atom pair; σ xy is the collision distance of the corresponding atom pair; r xy is the atomic spacing of the corresponding atom pair;
[0101] 5) The electrostatic potential function U ele is:
[0102]
[0103] Here, u e,x,y is the electrostatic potential function between any pair of the first atoms; the atomic charge number q x is the atomic charge number of the x-th first atom, and the atomic charge number q y is the atomic charge number of the y-th first atom;
[0104] Step 312, when the second option is the fluctuating charge model, correct the electrostatic potential function U tot of the total potential function U ele to obtain the corresponding first potential function and the first force field parameter set;
[0105] Specifically, it includes: Step 3121, correct the electrostatic potential function U tot of the total potential function U ele to:
[0106]
[0107] where the atomic charge variables Q x , Q y are the variable charge numbers of the two first atoms in the corresponding atom pair;
[0108] Step 3122, take the new total potential function U tot as the corresponding first potential function;
[0109] Step 3123, and use the bond stretching force constant k corresponding to all the first connection bonds in the first molecular system b,i and the standard bond length l 0,i , the bond angle bending force constant k corresponding to all the first bond angles θ,j and the standard bond angle θ 0,j , the dihedral angle torsion potential constant V corresponding to all the first dihedral angles n,m and the standard dihedral angle ω 0,m , the potential well depth ε corresponding to all atom pairs xy and the collision distance σ xy to form the corresponding first force field parameter set;
[0110] Step 313, when the second option is the Drude oscillator model, add Drude harmonic oscillators to the first molecular system to obtain a new first molecular system; and by adding the harmonic oscillator vibration potential function U tot to the total potential function U har-d and modifying the electrostatic potential function U ele to obtain the corresponding first potential function and first force field parameter set;
[0111] Specifically including: Step 3131, add Drude harmonic oscillators to the first molecular system to obtain a new first molecular system;
[0112] Specifically including: Based on the preset harmonic oscillator addition rule, add a Drude harmonic oscillator connected to it to each of some or all of the first atoms in the first molecular system, denoted as the corresponding first harmonic oscillator;
[0113] Among them, the particle attributes of the first harmonic oscillator include the paired atom identifier, the harmonic oscillator position coordinates, and the harmonic oscillator charge number; the atomic charge number of the first atom before adding the first harmonic oscillator is q0, the atomic charge number before adding the first harmonic oscillator is q1, and the harmonic oscillator charge number of the corresponding first harmonic oscillator is q2, then the corresponding relationship among the three charge numbers should be: q2 = q0 - q1;
[0114] Here, the harmonic oscillator addition rule is a preset rule that can be modified by the user according to actual needs; this rule stipulates which types of atoms in the molecular system can add harmonic oscillators. If the rule does not restrict the atom type, it means that harmonic oscillators need to be added to all atoms;
[0115] Step 3132, by adding the harmonic oscillator vibration potential function U tot to the total potential function U har-d and modifying the electrostatic potential function U ele to obtain the corresponding first potential function and first force field parameter set;
[0116] Specifically, it includes: Step 31321, setting the vibration potential function U of the harmonic oscillator har-d which is:
[0117]
[0118] where 1 ≤ o ≤ D, and D is the total number of the first harmonic oscillators; u har-d,o is the vibration potential function of the first harmonic oscillator; k d,o is the force constant of the corresponding first harmonic oscillator; r o is the distance between the corresponding first harmonic oscillator and its corresponding first atom;
[0119] Step 31322, adding the vibration potential function U of the harmonic oscillator har-d to the total potential function U tot to obtain a new total potential function U tot which is:
[0120] U tot = U bon + U ang + U tor + U vdW + U ele + U har-d ;
[0121] Step 31323, correcting the electrostatic potential function U tot of the new total potential function U ele to:
[0122]
[0123]
[0124] where 1 ≤ p ≤ D, 1 ≤ s ≤ N tom , 2 ≤ z ≤ N tom ; u e,o,p is the electrostatic potential function between any pair of the first harmonic oscillators; u e,o,s is the electrostatic potential function between any first harmonic oscillator and any first atom; u e,s,z is the electrostatic potential function between any pair of first atoms; the harmonic oscillator charge variable q o , q p are the variable charge numbers of their corresponding first harmonic oscillators; the atomic charge variable q s , q z are the variable charge numbers of their corresponding first atoms; r op is the distance between the corresponding two first harmonic oscillators; r os is the distance between the corresponding first harmonic oscillator and a first atom; r sz is the distance between the corresponding two first atoms;
[0125] Step 31323, take the new total potential energy function U tot as the corresponding first potential energy function; and from the bond stretching force constant k b,i corresponding to all the first connection bonds and the standard bond length l 0,i in the first molecular system, the bond angle bending force constant k θ,j corresponding to all the first bond angles and the standard bond angle θ 0,j , the dihedral angle torsion potential constant V n,m corresponding to all the first dihedral angles and the standard dihedral angle ω 0,m , the potential well depth ε xy corresponding to all atom pairs and the collision distance σ xy , and the force constant k d,o of all the first harmonic oscillators to form the corresponding first force field parameter set;
[0126] Step 314, when the second option is the induced dipole model, add the induced dipole potential energy function U tot to the total potential energy function U pol to obtain the corresponding first potential energy function and the first force field parameter set;
[0127] Specifically, it includes: Step 3141, set the induced dipole potential energy function U pol as:
[0128]
[0129]
[0130]
[0131] where 1 ≤ f, g ≤ N tom , g ≠ f; taking each first atom as an induced dipole point position, then u pol,f , u pol,g are the induced dipole potential energy functions of the corresponding f-th and g-th induced dipole point positions respectively; E 0,f is the induced electric field generated by the permanent charge of the first molecular system at the f-th induced dipole point position; α f is the polarizability tensor of the f-th induced dipole point position; T fg is the transformation matrix corresponding to the f-th and g-th induced dipole point positions; r fg is the distance between the f-th and g-th induced dipole point positions; I is the preset unit matrix; x, y, z are the three-dimensional rectangular coordinate components pointing from the f-th to the g-th induced dipole point position;
[0132] Step 3142, add the induced dipole potential energy function U pol to the total potential energy function U tot to obtain the new total potential energy function Utot is:
[0133] U tot = U bon + U ang + U tor + U vdW + U ele + U pol ;
[0134] Step 3143, take the new total potential function U tot as the corresponding first potential function; and from the bond stretching force constant k b,i corresponding to all first connecting bonds and the standard bond length l 0,i in the first molecular system, the bond angle bending force constant k θ,j corresponding to all first bond angles and the standard bond angle θ 0,j , the dihedral angle torsion potential constant V n,m corresponding to all first dihedral angles and the standard dihedral angle ω 0,m , the potential well depth ε xy corresponding to all atom pairs and the collision distance σ xy , the atomic charge number q of all first atoms, the induced electric field E 0,f corresponding to all induced dipole positions, form the corresponding first force field parameter set;
[0135] Step 32, and form the corresponding first molecular system polarization force field model from the first molecular system, the first potential function and the first force field parameter set.
[0136] Here, through the above steps 1-3, the embodiments of the present invention can automatically generate an adaptive polarization force field model, namely the first molecular system polarization force field model, based on the input molecular system, configuration optimization method option, and polarization model option.
[0137] It should be noted that after obtaining the first molecular system polarization force field model, the embodiments of the present invention can further perform parameter fitting on the first force field parameter set of the first molecular system polarization force field model. There are various implementation methods for the embodiments of the present invention to perform parameter fitting on the first force field parameter set. One implementation method is to perform parameter fitting on the first force field parameter set according to the iterative calculation method of the self-consistent field (SCF) ab initio method, in combination with the known particle properties of all atoms in the first molecular system; this type of method belongs to a relatively common calculation method, and the implementation details can be obtained by querying relevant technical literature, and will not be further elaborated here. There are also implementation methods such as performing force field parameter fitting based on the conjugate gradient method and performing force field parameter fitting based on the extended Lagrangian method, etc.
[0138] It should also be noted that in addition to implementing parameter fitting based on the above conventional methods, the embodiments of the present invention also provide an implementation method for parameter fitting based on model training, that is, parameter fitting processing is performed on the first force field parameter set of the model through a series of experimental observation data corresponding to the current first molecular system obtained by other means. The experimental observation data mentioned here are experimental molecular properties obtained through experimental tests, such as density, enthalpy of evaporation, surface tension, heat capacity, and dielectric constant. Specifically, the implementation steps for performing parameter fitting processing on the first force field parameter set of the first molecular system polarization force field model based on a series of experimental molecular properties are as follows:
[0139] Step A1: Compose a corresponding experimental molecular property set from all the obtained experimental molecular properties; use the first molecular system corresponding to the experimental molecular property set as the corresponding test molecular system; perform molecular dynamics simulation on each molecular property of the test molecular system based on the MD calculation method to obtain a corresponding simulated molecular property set; compose a test data from the experimental molecular property set and the corresponding simulated molecular property set; and compose a corresponding test data set from all the obtained test data;
[0140] Here, the embodiments of the present invention can simulate the simulated molecular properties corresponding to each experimental molecular property by calling a mature end-to-end model that takes experimental molecular properties as input and simulated molecular properties (or called calculated molecular properties) as output;
[0141] Step A2: Select the first test data from the test set as the current test data;
[0142] Step A3: Perform vector conversion on the experimental molecular property set and the simulated molecular property set of the current test data to obtain corresponding first experimental molecular property vector P exp {p exp,type} and first simulated molecular property vector P cal {p cal,type}; and regard the variables to be optimized in the first potential function of the first molecular system polarization force field model as one type of variables, and other variables as the second type of variables;
[0143] Among them, the first experimental molecular property vector P exp is composed of multiple first experimental molecular properties p exp,type Each first experimental molecular property p exp,type corresponds to a specific property type, such as density, enthalpy of evaporation, surface tension, heat capacity, and dielectric constant; the first simulated molecular property vector P cal is composed of multiple first simulated molecular properties p cal,type Each first simulated molecular property p cal,typecorresponds to a specific property type, and the first simulated molecular property p cal,type and the first experimental molecular property p exp,type are in one-to-one correspondence;
[0144] Step A4, set the objective function as F = Σ|p cal,type - p exp,type |; and estimate all first-class parameters in the first potential function in the direction of minimizing the objective function F, and form a corresponding first force field parameter prediction vector from the obtained estimated values;
[0145] Step A5, confirm whether the current test data is the last test data in the test set; if so, go to Step A6; if not, take the next test data in the test set as the current test data, and return to Step A3;
[0146] Step A6, record the vector length of the first force field parameter prediction vector as W, and record the total number of vectors of the first force field parameter prediction vector as H; and form a first parameter matrix with a shape of H×W from H first force field parameter prediction vectors;
[0147] wherein, the first parameter matrix includes H×W matrix units; each row in the first parameter matrix corresponds to a first force field parameter prediction vector;
[0148] Step A7, calculate the root mean square error for each column in the first parameter matrix so that each matrix unit in the first parameter matrix corresponds to a root mean square error value; and calculate the sum of all root mean square error values in each row to obtain the corresponding first row error sum, and take the first force field parameter prediction vector corresponding to the smallest first row error sum as the optimal parameter prediction vector; and assign values to the corresponding parameters in the first force field parameter set based on the estimated values of each first-class parameter in the optimal parameter prediction vector; and output the first force field parameter set with the parameter assignment completed as the processing result of this parameter fitting.
[0149] Figure 2 This is the module structure diagram of a processing device for constructing a polarization force field model provided in the second embodiment of the present invention. The device is a terminal device, a server or a system for implementing the foregoing method embodiment, or can also be a device that enables the foregoing terminal device, server or system to implement the foregoing method embodiment. For example, the device can be a device or a chip system of the foregoing terminal device, server or system. As Figure 2 shown, the device includes: a data receiving module 201, a configuration optimization module 202, and a model construction module 203.
[0150] The data receiving module 201 is configured to receive a molecular system, a configuration optimization method option, and a polarization model option as a corresponding first molecular system, a first option, and a second option respectively; the first molecular system includes a plurality of first molecules and a plurality of first connecting bonds; each first molecule includes a plurality of first atoms; the particle attributes of the first atoms include atomic element type, atomic mass, atomic position coordinates, and atomic charge number; the first connecting bonds are used to connect two first atoms; the bond attributes of the first connecting bonds include bond types; the first option includes Hartree-Fock method, density functional method, perturbation theory method, and coupled cluster method; the second option includes fluctuating charge model, Drude oscillator model, and induced dipole model.
[0151] The configuration optimization module 202 is configured to perform structure optimization processing on the first molecular system based on the first option.
[0152] The model construction module 203 is configured to construct a polarization force field potential function according to the second option to obtain a corresponding first potential function and a first set of force field parameters; and form a corresponding first molecular system polarization force field model from the first molecular system, the first potential function, and the first set of force field parameters.
[0153] A processing device for constructing a polarization force field model provided by an embodiment of the present invention can execute the method steps in the above method embodiment, and its implementation principle and technical effects are similar, which will not be elaborated here.
[0154] It should be noted that it should be understood that the division of each module of the above device is only a logical function division. In actual implementation, it can be fully or partially integrated into a physical entity, or physically separated. And these modules can all be implemented in the form of software called by a processing element; they can also all be implemented in the form of hardware; or some modules can be implemented in the form of software called by a processing element, and some modules can be implemented in the form of hardware. For example, the data receiving module can be a separately established processing element, or can be integrated in a certain chip of the above device. In addition, it can also be stored in the memory of the above device in the form of program code, and called and executed by a certain processing element of the above device to perform the functions of the above determined modules. The implementation of other modules is similar. In addition, these modules can be fully or partially integrated together or independently implemented. The processing element described here can be an integrated circuit with signal processing capabilities. In the implementation process, each step of the above method or each of the above modules can be completed by the integrated logic circuit in the processor element in hardware or in the form of instructions in software.
[0155] For example, the above-mentioned modules can be one or more integrated circuits configured to implement the above methods. For example: one or more Application Specific Integrated Circuits (ASICs), or, one or more Digital Signal Processors (DSPs), or, one or more Field Programmable Gate Arrays (FPGAs), etc. Again, when a certain module above is implemented in the form of a processing element scheduler code, the processing element can be a general-purpose processor, such as a Central Processing Unit (CPU) or other processors that can call program code. Again, these modules can be integrated together and implemented in the form of a System-on-a-chip (SOC).
[0156] In the above embodiments, it can be implemented in whole or in part by software, hardware, firmware, or any combination thereof. When implemented using software, it can be implemented in whole or in part in the form of a computer program product. The computer program product includes one or more computer instructions. When the computer program instructions are loaded and executed on a computer, the processes or functions described in the foregoing method embodiments are generated in whole or in part. The above computer can be a general-purpose computer, a special-purpose computer, a computer network, or other programmable devices. The above computer instructions can be stored in a computer-readable storage medium, or transmitted from one computer-readable storage medium to another. For example, the above computer instructions can be transmitted from a website, computer, server, or data center to another website, computer, server, or data center in a wired manner (such as coaxial cable, optical fiber, Digital Subscriber Line (DSL)) or wirelessly (such as infrared, wireless, Bluetooth, microwave, etc.). The above computer-readable storage medium can be any available medium that a computer can access or a data storage device such as a server or data center that includes one or more integrated available media. The above available medium can be a magnetic medium (for example, a floppy disk, a hard disk, a magnetic tape), an optical medium (for example, a DVD), or a semiconductor medium (for example, a solid state disk (SSD)), etc.
[0157] Figure 3 It is a schematic structural diagram of an electronic device provided in Embodiment 3 of the present invention. The electronic device can be a terminal device or a server that implements the method of the foregoing embodiments, or can be a terminal device or a server that is connected to the foregoing terminal device or server and implements the method of the foregoing embodiments. As Figure 3As shown, the electronic device may include: a processor 301 (such as a CPU), a memory 302, and a transceiver 303; the transceiver 303 is coupled to the processor 301, and the processor 301 controls the transceiver operations of the transceiver 303. Various instructions may be stored in the memory 302 for completing various processing functions and implementing the processing steps described in the method of the foregoing embodiments. Preferably, the electronic device according to the embodiment of the present invention further includes: a power supply 304, a system bus 305, and a communication port 306. The system bus 305 is used to implement communication connections between components. The communication port 306 is used for the electronic device to communicate and connect with other peripherals.
[0158] As mentioned in Figure 3 the system bus 305 may be a Peripheral Component Interconnect (PCI) bus or an Extended Industry Standard Architecture (EISA) bus, etc. The system bus may be divided into an address bus, a data bus, a control bus, etc. For the sake of convenience of representation, only a thick line is used in the figure, but it does not mean that there is only one bus or one type of bus. The communication interface is used to implement communication between the database access device and other devices (such as clients, read-write libraries, and read-only libraries). The memory may include a Random Access Memory (RAM), and may also include a non-volatile memory, such as at least one disk memory.
[0159] The foregoing processor may be a general-purpose processor, including a Central Processing Unit (CPU), a Network Processor (NP), a Graphics Processing Unit (GPU), etc.; it may also be a Digital Signal Processor (DSP), an Application Specific Integrated Circuit (ASIC), a Field Programmable Gate Array (FPGA), or other programmable logic devices, discrete gate or transistor logic devices, discrete hardware components.
[0160] It should be noted that the embodiment of the present invention further provides a computer-readable storage medium, in which instructions are stored, and when the instructions are run on a computer, the computer is caused to execute the methods and processing procedures provided in the foregoing embodiments.
[0161] The embodiment of the present invention further provides a chip for running instructions, and the chip is used to execute the processing steps described in the foregoing method embodiments.
[0162] The embodiments of the present invention provide a processing method, apparatus, electronic device, and computer-readable storage medium for constructing a polarization force field model; the present invention provides four configuration optimization methods for selection: the Hartree-Fock method, the density functional method, the perturbation theory method, and the coupled cluster method, and provides three polarization models for selection: the fluctuating charge model, the Drude oscillator model, and the induced dipole model; and perform configuration optimization on the molecular system to be processed based on the configuration optimization method selected by the user, and construct the polarization force field potential function based on the polarization model selected by the user; and construct the force field parameter set based on the optimized molecular system and the polarization force field potential function of the specified model, and the corresponding polarization force field model output is composed of the obtained optimized molecular system, force field potential function, and force field parameter set. Through the present invention, on the one hand, the rationality of the molecular system structure is improved based on configuration optimization, on the other hand, the configuration richness and configuration accuracy of the polarization force field model are improved through the standard processing flow of the three polarization models, and on the third hand, the human limitation is eliminated and the processing efficiency is improved.
[0163] Those skilled in the art should also be able to further realize that the units and algorithm steps of each example described in combination with the embodiments disclosed herein can be implemented by electronic hardware, computer software, or a combination of the two. To clearly illustrate the interchangeability of hardware and software, the composition and steps of each example have been generally described according to functions in the above description. Whether these functions are executed in a hardware or software manner depends on the specific application and design constraints of the technical solution. Those skilled in the art can use different methods to implement the described functions for each specific application, but such implementation should not be considered to exceed the scope of the present invention.
[0164] The steps of the method or algorithm described in combination with the embodiments disclosed herein can be implemented by hardware, a software module executed by a processor, or a combination of the two. The software module can be placed in a random access memory (RAM), memory, read-only memory (ROM), electrically programmable ROM, electrically erasable programmable ROM, register, hard disk, removable disk, CD-ROM, or any other form of storage medium well-known in the technical field.
[0165] The specific embodiments described above further elaborate the purpose, technical solution, and beneficial effects of the present invention. It should be understood that the above description is only the specific embodiments of the present invention and is not used to limit the protection scope of the present invention. Any modification, equivalent replacement, improvement, etc. made within the spirit and principle of the present invention shall be included in the protection scope of the present invention.
Claims
1. A processing method for constructing a polarization force field model, characterized in that: The method comprises: A molecular system, a configuration optimization method option, and a polarization model option are received as corresponding first molecular systems, first options, and second options; the first molecular system includes a plurality of first molecules and a plurality of first connecting bonds; the first molecules include a plurality of first atoms; the particle properties of the first atoms include atomic element type, atomic mass, atomic position coordinates, and atomic charge number; the first connecting bond is used to connect two of the first atoms; the bond properties of the first connecting bond include a connecting bond type; the first option includes a Hartree-Fock method, a density functional method, a perturbation theory method, and a coupled cluster method; the second option includes a fluctuation charge model, a Drude oscillator model, and an induced dipole model; Performing structural optimization processing on the first molecular system based on the first option; According to the second option, a polarization force field potential function is constructed to obtain a corresponding first potential function and a first force field parameter set; and the first molecular system, the first potential function and the first force field parameter set form a corresponding first molecular system polarization force field model; The step of constructing the polarization force field potential function according to the second option to obtain the corresponding first potential function and first force field parameter set specifically includes: Set the total potential function U tot =U bon +U ang +U tor +U vdw +U ele Among them, U bon is the bond stretching potential function, U ang is the bond angle bending potential function, U tor is the dihedral angle torsion potential function, U vdW is the van der Waals potential function, U ele is the electrostatic potential function; When the second option is the fluctuating charge model, the total potential function U tot The electrostatic potential function U ele Correcting to obtain the corresponding first potential function and the first force field parameter set; When the second option is a Drude oscillator model, a Drude oscillator is added to the first molecular system to obtain a new first molecular system; and by adding the total potential function U tot Add the oscillator vibration potential function U har-d And the electrostatic potential function U ele Correcting to obtain the corresponding first potential function and the first force field parameter set; When the second option is the induced dipole model, the total potential function U tot Add the induced dipole potential function U pol The corresponding first potential function and the first force field parameter set are obtained.
2. The processing method for constructing a polarization force field model according to claim 1, characterized in that: The performing structural optimization processing on the first molecular system based on the first option specifically includes: When the first option is the Hartree-Fock method, performing structural optimization on the first molecular system based on HF / 2-zeta, HF / 3-zeta or HF / 4-zeta calculation; When the first option is a density functional method, performing structural optimization on the first molecular system based on B3LYP / 2-zeta, B3LYP / 3-zeta or B3LYP / 4-zeta calculation; When the first option is a perturbation theory method, performing structural optimization on the first molecular system based on MP2 / 2-zeta, MP2 / 3-zeta or MP2 / 4-zeta calculation; When the first option is the coupled cluster method, the structure of the first molecular system is optimized based on CCSD(T) / 2-zeta or CCSD(T) / 3-zeta calculation.
3. The processing method for constructing a polarization force field model according to claim 1, characterized in that: The bond stretching potential function U bon for: Wherein, 1≤i≤B, A is the total number of the first connecting keys; u b,i k is the bond stretching potential function of any of the first connecting bonds; b,i is the bond stretching force constant of the corresponding first connecting bond; the standard bond length l 0,i is the bond length value of the first connecting bond in the equilibrium state; bond length variable l i is the variable key length value of the corresponding first connection key; The bond angle bending potential function U ang for: Wherein, 1≤j≤B, B is the total number of first bond angles, and the first bond angle is the angle between two first connecting bonds consisting of three sequentially connected first atoms; u a,j k is the bond angle bending potential function of any of the first bond angles; θ,j is the bond angle bending force constant corresponding to the first bond angle; standard bond angle θ 0,j is the angle value of the first bond angle in the equilibrium state, and the bond angle variable θ j is the variable angle value of the corresponding first bond angle; The dihedral torsion potential function U tor for: Wherein, 1≤m≤C, C is the total number of first dihedral angles, and the first dihedral angle is the angle between two first intersecting planes formed by three first connecting bonds composed of four sequentially connected first atoms; u t,m is the dihedral angle torsion potential function of any of the first dihedral angles; the constant n is the number of times the energy minimum occurs when the bond rotates 360°; V n,m is the dihedral angle torsion potential constant of the first dihedral angle; standard dihedral angle ω 0,m is the angle value of the first dihedral angle in the equilibrium state, and the standard dihedral angle ω 0,m The values of include 0 and π; the dihedral angle variable ω m is the variable angle value of the corresponding first dihedral angle; The van der Waals potential function U vdW for: Where 1≤x≤N tom , 2≤y≤N tom , N tom is the total number of the first atoms; u v,x,y is the van der Waals potential function between any pair of the first atoms; ε xy is the potential well depth of the corresponding atomic pair; σ xy is the collision distance of the corresponding atomic pair; r xy is the interatomic distance between the corresponding atomic pairs; The electrostatic potential function U ele for: Among them, u e,x,y is the electrostatic potential function between any pair of the first atoms; the atomic charge number q x is the atomic charge number of the xth atom in the first atom, and the atomic charge number q y is the atomic charge number of the yth first atom.
4. The processing method for constructing a polarization force field model according to claim 3, characterized in that: The total potential function U tot The electrostatic potential function U ele Correction is performed to obtain the corresponding first potential function and the first force field parameter set, specifically including: The total potential function U tot The electrostatic potential function U ele Corrected to: Among them, the atomic charge variable Q x , Q y is the variable charge number of the two first atoms in the corresponding atomic pair; The new total potential function U tot As the corresponding first potential function; and the bond stretching force constant k corresponding to all the first connecting bonds in the first molecular system b,i and the standard bond length l 0,i , the bond angle bending force constant k corresponding to all the first bond angles θ,j and the standard bond angle θ 0,j , the dihedral angle torsion potential constant V corresponding to all the first dihedral angles n,m and the standard dihedral angle ω 0,m , the potential well depth ε corresponding to all atomic pairs xy and the collision distance σ xy Form the corresponding first force field parameter set.
5. The processing method for constructing a polarization force field model according to claim 3, characterized in that: The step of performing Drude resonator addition on the first molecular system to obtain a new first molecular system specifically includes: Based on the preset oscillator adding rule, a Drude oscillator connected to some or all of the first atoms in the first molecular system is added and recorded as the corresponding first oscillator; the particle properties of the first oscillator include the paired atom identifier, the oscillator position coordinates and the oscillator charge number; the atomic charge number of the first atom before adding the first oscillator is q0, the atomic charge number before adding the first oscillator is q1, and the oscillator charge number of the corresponding first oscillator is q2, then the corresponding relationship between the three charge numbers should be: q2=q0-q1.
6. The processing method for constructing a polarization force field model according to claim 5, characterized in that: The total potential function U tot Add the oscillator vibration potential function U har-d And the electrostatic potential function U ele Correction is performed to obtain the corresponding first potential function and the first force field parameter set, specifically including: Set the oscillator vibration potential function U har-d for: Wherein, 1≤o≤D, D is the total number of the first resonators; u har-d,o k is the oscillator vibration potential function of the first oscillator; d,o is the force constant of the first harmonic oscillator; r o is the distance between the corresponding first harmonic oscillator and its corresponding first atom; The oscillator vibration potential function U har-d Add to the total potential function U tot Get the new total potential function U tot For: U tot =U bon +U ang +U tor +U vdW +U ele +U har-d ; The new total potential function U tot The electrostatic potential function U ele Corrected to: Among them, 1≤p≤D, 1≤s≤N tom , 2≤z≤N tom ;u e,o,p is the electrostatic potential function between any pair of the first resonators; u e,o,s is the electrostatic potential function between any of the first resonators and any of the first atoms; u e,s,z is the electrostatic potential function between any pair of the first atoms; the oscillator charge variable q o ,q p is the variable charge number of the first harmonic oscillator corresponding to each other; the atomic charge variable q s ,q z is the variable charge number of the first atom corresponding to each other; r op is the distance between the two corresponding first resonators; r os is the distance between the first harmonic oscillator and one of the first atoms; r sz is the distance between the two corresponding first atoms; The new total potential function U tot As the corresponding first potential function; and the bond stretching force constant k corresponding to all the first connecting bonds in the first molecular system b,i and the standard bond length l 0,i , the bond angle bending force constant k corresponding to all the first bond angles θ,j and the standard bond angle θ 0,j , the dihedral angle torsion potential constant V corresponding to all the first dihedral angles n,m and the standard dihedral angle ω 0,m , the potential well depth ε corresponding to all atomic pairs xy and the collision distance σ xy , the force constant k of all the first harmonic oscillators d,o Form the corresponding first force field parameter set.
7. The processing method for constructing a polarization force field model according to claim 3, characterized in that: The total potential function U tot Add the induced dipole potential function U pol Obtaining the corresponding first potential function and the first force field parameter set specifically includes: Set the induced dipole potential function U pol for: Where 1≤f, g≤N tom , g≠f; taking each of the first atoms as an induced dipole point, then u pol,f 、u pol,g are the induced dipole potential functions of the corresponding f-th and g-th induced dipole points, respectively; E 0,f is the induced electric field generated by the permanent charge of the first molecular system at the fth induced dipole point; α f is the polarizability tensor of the fth induced dipole point; T fg is the transformation matrix corresponding to the fth and gth induced dipole points; r fg is the distance between the fth and gth induced dipole points; I is a preset unit matrix; x, y, z are the three-dimensional rectangular coordinate components pointing from the fth to the gth induced dipole point; The induced dipole potential function U pol Add to the total potential function U tot Get the new total potential function U tot For: U tot =U bon +U ang +U tor +U vdW +U ele +U pol ; The new total potential function U tot As the corresponding first potential function; and the bond stretching force constant k corresponding to all the first connecting bonds in the first molecular system b,i and the standard bond length l 0,i , the bond angle bending force constant k corresponding to all the first bond angles θ,j and the standard bond angle θ 0,j , the dihedral angle torsion potential constant V corresponding to all the first dihedral angles n,m and the standard dihedral angle ω 0,m , the potential well depth ε corresponding to all atomic pairs xy and the collision distance σ xy , the atomic charge number q of all the first atoms, the induced electric field E corresponding to all the induced dipole points 0,f Form the corresponding first force field parameter set.
8. A device for executing the processing method for constructing a polarization force field model according to any one of claims 1 to 7, characterized in that: The device comprises: a data receiving module, a configuration optimization module and a model building module; The data receiving module is used to receive a molecular system, a configuration optimization method option, and a polarization model option as the corresponding first molecular system, a first option, and a second option; the first molecular system includes a plurality of first molecules and a plurality of first connecting bonds; the first molecule includes a plurality of first atoms; the particle properties of the first atoms include atomic element type, atomic mass, atomic position coordinates, and atomic charge number; the first connecting bond is used to connect two of the first atoms; the bond properties of the first connecting bond include a connecting bond type; the first option includes a Hartree-Fock method, a density functional method, a perturbation theory method, and a coupled cluster method; the second option includes a fluctuation charge model, a Drude oscillator model, and an induced dipole model; The configuration optimization module is used to perform structural optimization processing on the first molecular system based on the first option; The model construction module is used to construct the polarization force field potential function according to the second option to obtain the corresponding first potential function and the first force field parameter set; and the first molecular system, the first potential function and the first force field parameter set form the corresponding first molecular system polarization force field model.
9. An electronic device, characterized in that: include: memory, processors, and transceivers; The processor is used to couple with the memory, read and execute instructions in the memory, so as to implement the method according to any one of claims 1 to 7; The transceiver is coupled to the processor, and the processor controls the transceiver to send and receive messages.
10. A computer-readable storage medium, characterized in that: The computer-readable storage medium stores computer instructions, and when the computer instructions are executed by a computer, the computer is enabled to execute the method according to any one of claims 1 to 7.
Citation Information
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Method and application for constructing polarized force fields and method and system for predicting drug crystal forms
CN106372400A