All-atom molecular dynamics simulation method and system of double-plate limited system based on AMOEBA force field
The dual-plane limited simulation system is constructed through the AMOEBA force field and mirror charge method, which solves the problem that traditional force fields cannot capture polarization response, realizes high-precision ion distribution simulation, and improves the performance of energy storage devices.
Patent Information
- Application Number
- CN202510289895.3
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- Filing Date
- 2025-03-12
- Publication Date
- 2025-07-04
AI Technical Summary
The traditional non-polarization force field cannot dynamically capture the polarization response of atoms, resulting in significant deviations in predicting the distribution of ions at the table interface, affecting the performance of energy storage devices.
AMOEBA polarizable force field is adopted and combined with the mirror charge method, by constructing a dual-plane limited simulation system, the system density balance is performed, and the plate dipole correction term is added, NVT simulation is performed, and mirror atoms are added to simulate the conductor surface polarization effect.
It achieves higher simulation accuracy, significantly improves the high-precision characterization capabilities of the electric double layer structure and ion distribution of the conductor/electrolyte interface, and provides a foundation for optimizing the performance of energy storage devices.
Smart Images
Figure CN120260699A_ABST
Abstract
Description
Technical Field
[0001] The present invention relates to the field of computer simulation technology, and in particular to a method and system for all-atom molecular dynamics simulation of a double-plate confined system based on the AMOEBA force field. Background Art
[0002] Double-conductor plate confined systems widely exist in energy storage devices such as supercapacitors and ion batteries. As the core component of energy storage devices, the electrolyte not only determines the ion mobility and charge transfer efficiency, but its ion distribution at the interface directly affects the electric double layer structure and energy storage density. In such systems, the polarization effect at the electrode / electrolyte interface (such as surface polarization caused by the redistribution of free charges in the conductor) will change the interface electric field distribution, significantly affecting the adsorption behavior of electrolyte ions and the formation of the electric double layer, and further affecting the power density and cycle stability of the device. Therefore, in-depth understanding of the influence of surface and interface polarization effects on the electrolyte electric double layer is of great significance for optimizing the performance of energy storage devices. In recent years, with the continuous development of computer technology and simulation methods, all-atom molecular dynamics simulation has made it possible for us to understand the formation mechanism of the electrolyte electric double layer at the molecular level. By combining the particle mesh Ewald (PME) algorithm and the method of image charges, molecular dynamics simulation can quickly and accurately describe the additional long-range electrostatic interactions generated by surface polarization. However, traditional non-polarizable force fields use the fixed charge approximation and cannot dynamically capture the polarization response of atoms (such as changes in induced dipole moments), resulting in significant deviations in predicting the ion distribution at the surface and interface. Summary of the Invention
[0003] Aiming at the above problems, the purpose of the present invention is to provide a method and system for all-atom molecular dynamics simulation of a double-plate confined system based on the AMOEBA force field, which can achieve higher simulation accuracy and significantly improve the high-precision characterization ability of the electric double layer structure and ion distribution at the conductor / electrolyte interface.
[0004] To achieve the above object, in a first aspect, the technical solution adopted by the present invention is as follows: A method for all-atom molecular dynamics simulation of a double-plate confined system based on the AMOEBA force field, which includes: constructing a double-plate confined simulation system, and processing the force field parameters of the atoms constituting the plate to be applicable to the double-plate confined simulation system; for the double-plate confined simulation system, performing pressure control simulation along the normal direction of the conductor plane under a set temperature and pressure by Monte Carlo barostat to balance the system density; adding a plate dipole correction term under the AMOEBA force field to the system after density balance, and performing NVT simulation without surface polarization at a set temperature; where the NVT simulation is a canonical ensemble simulation; in the system after density balance, adding mirror atoms symmetric to the plate for each atom, setting corresponding AMOEBA force field parameters for the mirror atoms, and then performing NVT simulation with conductor surface polarization effect at a set temperature.
[0005] Further, constructing a double-plate confined simulation system and processing the force field parameters of the atoms constituting the plate includes:
[0006] Constructing a simulation box, setting the charges and masses of the plate atoms to 0, removing the bonds of the plate atoms, and only retaining the van der Waals interactions between the plate atoms and the atoms in the confined system.
[0007] Further, for the double-plate confined simulation system, performing pressure control simulation along the normal direction of the conductor plane under a set temperature and pressure by Monte Carlo barostat to balance the system density includes:
[0008] Scaling the size of the simulation box along the normal direction of the plate;
[0009] Moving the plates and the molecules in the confined system in the system proportionally according to the change in the size of the box along the normal direction of the plate to obtain a new double-plate confined simulation system with the new size;
[0010] Calculating the potential energy difference between the new and old systems, and using the Metropolis method to determine whether to accept this movement; if accepted, performing molecular dynamics simulation for a set number of steps to balance the new system; otherwise, reverting to the previous old system;
[0011] Repeating the above process until the currently set number of simulation steps is reached.
[0012] Further, scaling the size of the simulation box along the normal direction of the plate specifically means: generating a random number R, setting the scaling size according to the random number R, and scaling the entire simulation box in the z direction by the set scaling size.
[0013] Further, adding a plate dipole correction term under the AMOEBA force field to the system after density balance and performing NVT simulation without surface polarization at a set temperature includes:
[0014] Calculate the dipole moment M of the computing system in the direction normal to the flat plate z ;
[0015] Add a correction force F for each example z,i After that, perform one step of molecular dynamics simulation, and determine whether the currently set number of simulation steps has been completed. If it is completed, the simulation of the system without surface polarization effect is completed. Otherwise, recalculate the dipole moment M of the system in the direction normal to the flat plate z .
[0016] Furthermore, to correct the system without surface polarization, a correction force needs to be added to the force on each atom in the z direction at each molecular simulation step. The correction force is:
[0017]
[0018] In the formula, F z,i is the correction force; q i is the charge of the atom; ∈0 is the vacuum permittivity; V is the total volume of the system; N is the total number of atoms in the system; z i is the z coordinate of the atom, is the permanent dipole moment of the atom, is the induced dipole moment of the atom
[0019] Furthermore, in the system after density equilibration, add a mirror image atom symmetric to the flat plate for each atom, and set the corresponding AMOEBA force field parameters for the mirror image atom. Then, perform NVT simulation with conductor surface polarization effect at the set temperature, including:
[0020] Add a mirror image atom for each real atom, and set the force field parameters of each mirror image atom in turn: set the mass of the mirror image atom to 0; remove all its bonding terms; the force field parameters of the van der Waals interaction are the same as those of its real atom; the charge is the same as that of its real atom but with the opposite sign, and the x and y components of the permanent dipole moment and permanent quadrupole moment in the global coordinate system are partially opposite; the induced dipole parameters are the same as those of its real atom;
[0021] After each molecular simulation step is executed, move each mirror image atom in turn to ensure that each mirror image atom is mirror symmetric to its real atom with respect to the flat plate at z = 0, and complete the simulation of the system with conductor polarization effect
[0022] Second aspect, the technical solution adopted by the present invention is as follows: A full-atom molecular dynamics simulation system for a double-plate confined system based on the AMOEBA force field, which includes: a processing module, constructing a double-plate confined simulation system and processing the force field parameters of the atoms constituting the plate to be applicable to this double-plate confined simulation system; a density equilibrium module, for the double-plate confined simulation system, performing pressure control simulation along the normal direction of the conductor plane using Monte Carlo barostat at a set temperature and pressure to achieve system density equilibrium; an NVT simulation module without surface polarization, adding a plate dipole correction term under the AMOEBA force field to the system after density equilibrium and performing NVT simulation without surface polarization at a set temperature; where, the NVT simulation is a canonical ensemble simulation; an NVT simulation module with conductor surface polarization effect, in the system after density equilibrium, adding mirror atoms symmetric to the plate for each atom and setting corresponding AMOEBA force field parameters for the mirror atoms, and then performing NVT simulation with conductor surface polarization effect at a set temperature.
[0023] Third aspect, the technical solution adopted by the present invention is as follows: A computer-readable storage medium storing one or more programs, the one or more programs including instructions that, when executed by a computing device, cause the computing device to execute any of the above methods.
[0024] Fourth aspect, the technical solution adopted by the present invention is as follows: A computing device, which includes: one or more processors, a memory, and one or more programs, where the one or more programs are stored in the memory and configured to be executed by the one or more processors, and the one or more programs include instructions for executing any of the above methods.
[0025] Due to the above technical solutions adopted by the present invention, it has the following advantages:
[0026] Through the technical solution of the full-atom molecular dynamics simulation of the double-plate confined system based on the AMOEBA force field provided by the present invention, a tunable (on / off) conductor surface polarization simulation is realized, filling the gap in the simulation method for this system under the AMOEBA force field. Compared with traditional non-polarized force fields, the present invention combined with the AMOEBA force field can achieve higher simulation accuracy, significantly improving the high-precision characterization ability of the double-layer structure and ion distribution at the conductor / electrolyte interface, laying a foundation for further studying the influence of surface polarization on the structure and properties of electrolytes. Description of the Drawings
[0027] Figure 1 is the overall flowchart of the full-atom molecular dynamics simulation method for the double-plate confined system based on the AMOEBA force field in the embodiment of the present invention;
[0028] Figure 2It is a detailed flowchart of the all-atom molecular dynamics simulation method for the double-plate confined system based on the AMOEBA force field in the embodiments of the present invention;
[0029] Figure 3 It is a schematic diagram of the construction method of the double-plate simulation system adopted in the embodiments of the present invention;
[0030] Figure 4 It is a schematic diagram of the double-conductor plate confined simulation system under the surface polarization effect (the left side in the figure is the mirror atom, and the right side is the real atom) in the embodiments of the present invention;
[0031] Figure 5 It is the Li + and Cl - ion concentration distribution diagrams along the z-axis direction obtained by taking the 0.9M LiCl aqueous solution as an example in the simulation method of the embodiments of the present invention. Detailed implementation manners
[0032] Compared with the traditional non-polarizable force field using the fixed charge approximation, the AMOEBA polarizable force field introduces the high-order multipole and polarizable atomic charge model, which can accurately describe the electron induction and charge penetration effects, and provides a more realistic physical model for the strongly polarizable charged system of electrolytes. However, its complex force field form and computational requirements significantly increase the simulation difficulty, especially when dealing with the coupling problem of the conductor surface polarization effect and the dynamic interaction of electrolytes. Therefore, the present invention proposes an all-atom molecular dynamics simulation method and system for the double-plate confined system based on the AMOEBA force field. The present invention adopts an efficient simulation method applicable to the AMOEBA polarizable force field, which not only meets the technical requirements of high-precision calculation for such systems, but also provides a basis for deeply analyzing the influence of the surface polarization effect on the electrolyte interface behavior, so as to further guide the interface design and optimization of high-performance energy storage devices.
[0033] The present invention includes: 1) constructing a double-plate confined simulation system and processing the AMOEBA force field parameters of the plate atoms; 2) for the system obtained in step 1), performing the system density equilibrium by using the Monte Carlo barostat to control the pressure along the normal direction of the conductor plate plane under the set temperature and pressure; 3) adding the plate dipole correction term under the AMOEBA force field to the system obtained in step 2) and performing the canonical ensemble (NVT) simulation without the surface polarization effect; 4) adding mirror atoms symmetric to the conductor plate for each atom in the system obtained in step 2), setting the corresponding AMOEBA force field parameters for the mirror atoms, and then performing the NVT simulation with the conductor surface polarization effect. The present invention can achieve the efficient simulation of the plate-confined electrolyte system under the AMOEBA polarizable force field.
[0034] To make the objectives, technical solutions, and advantages of the embodiments of the present invention clearer, the technical solutions of the embodiments of the present invention will be clearly and completely described below with reference to the accompanying drawings of the embodiments of the present invention. Obviously, the described embodiments are some, but not all, of the embodiments of the present invention. All other embodiments obtained by those of ordinary skill in the art based on the described embodiments of the present invention fall within the scope of protection of the present invention.
[0035] It should be noted that the terms used herein are only for describing specific embodiments and are not intended to limit the exemplary embodiments according to the present invention. As used herein, unless the context clearly indicates otherwise, the singular form is also intended to include the plural form. In addition, it should be understood that when the terms "comprise" and / or "include" are used in this specification, they indicate the presence of features, steps, operations, devices, components, and / or combinations thereof.
[0036] In one embodiment of the present invention, a full-atom molecular dynamics simulation method for a double-plate confined system based on the AMOEBA force field is provided. In this embodiment, as Figure 1 、 Figure 2 shown, the method includes the following steps:
[0037] 1) Construct a double-plate confined simulation system and process the force field parameters of the atoms constituting the plates to be applicable to this double-plate confined simulation system;
[0038] 2) For the double-plate confined simulation system, at the set temperature and pressure, use Monte Carlo barostat along the conductor plane Carry out normal direction pressure control simulation to balance the system density;
[0039] 3) Add the plate dipole correction term under the AMOEBA force field to the system after density balance and perform NVT simulation without surface polarization at a set temperature; where the NVT simulation is a canonical ensemble simulation;
[0040] 4) In the system after density balance, add mirror atoms symmetric to the plate for each atom, set corresponding AMOEBA force field parameters for the mirror atoms, and then perform NVT simulation with conductor surface polarization effect at a set temperature.
[0041] In the above step 1), constructing a double-plate confined simulation system and processing the force field parameters of the atoms constituting the plates specifically means:
[0042] Construct a simulation box, set the charges and masses of the plate atoms to 0, remove the bonding of the plate atoms, and only retain the van der Waals interaction between the plate atoms and the atoms in the confined system.
[0043] In this embodiment, for example, construct a simulation box with size (L x , L y , 2Lz ) The simulated box, with two parallel plates placed on the x-y plane at z = 0 and z = L respectively, and the confined system is placed between the two plates; the mass and charge of the plate atoms are set to 0, and their bonding is removed, only retaining the van der Waals interaction with the atoms in the confined system. z In step 2) above, for the double-plate confined simulation system, under the set temperature and pressure, Monte Carlo barostat is used to control the pressure along the normal direction of the conductor plane for simulation to balance the system density, including the following steps:
[0044] 2.1) Scale the size of the simulation box along the normal direction of the plate;
[0045] In this embodiment, specifically: for example, generate a random number R between (-1, 1), and set the scaling size according to the random number R to scale the entire simulation box in the z direction by the set scaling size. For example, scale the size of the entire simulation box in the z direction by 0.01R times.
[0046] 2.2) Move the molecules of the plates and the confined system in the system proportionally according to the change in the size of the box along the normal direction of the plate to obtain a double-plate confined simulation system under the new size;
[0047] 2.3) Calculate the potential energy difference between the new and old systems, and use the Metropolis method to judge whether to accept this movement; if accepted, perform molecular dynamics simulation for a set number of steps to balance the new system; otherwise, return to the previous old system;
[0048] 2.4) Repeat the process of steps 2.1) to 2.3) above until the currently set number of simulation steps is reached.
[0049] In step 3) above, add the plate dipole correction term under the AMOEBA force field to the system after density balance, and perform NVT simulation without surface polarization at the set temperature, including the following steps:
[0050] 3.1) Calculate the dipole moment M of the system in the normal direction of the plate
[0051] 3.2) Add a correction force F to each example z ;
[0052] 3.3) After that, perform one step of molecular dynamics simulation, and judge whether the currently set number of simulation steps has been completed. If completed, the simulation of the system without surface polarization effect is completed; otherwise, recalculate the dipole moment M of the system in the normal direction of the plate z,i 3.4) Add a correction force to the force on each of the atoms in the z direction. This correction force is: z
[0053] In this embodiment, to correct the system without surface polarization, specifically, at each molecular simulation step, for each
[0054]
[0055] where, F z,i is the correction force; q i is the charge of the atom; ∈0 is the vacuum permittivity; V is the total volume of the system; N is the total number of atoms in the system; z i is the z - coordinate of the atom, is the permanent dipole moment of the atom, is the induced dipole moment of the atom.
[0056] In step 4) above, in the system after density equilibration, for each atom, add a mirror atom symmetric about the flat plate, and set the corresponding AMOEBA force field parameters for this mirror atom. Then, perform an NVT simulation with the conductor surface polarization effect at the set temperature, including the following steps:
[0057] 4.1) Add a mirror atom for each real atom, and sequentially set the force field parameters of each mirror atom: set the mass of the mirror atom to 0; remove all its bonding terms; the force field parameters of the van der Waals interaction are the same as those of its real atom; the charge is the same as that of its real atom but with the opposite sign, and the x and y components of the permanent dipole moment and the permanent quadrupole moment in the global coordinate system are partially opposite; the induced dipole parameters are the same as those of its real atom;
[0058] 4.2) After each molecular simulation step is executed, sequentially move each mirror atom to ensure that each mirror atom is mirror - symmetric with its real atom about the flat plate at z = 0, thus completing the simulation of the system with the conductor polarization effect.
[0059] Example: Taking a 0.9M LiCl aqueous solution confined between two graphene flat plates as an example, the specific implementation steps of the above simulation method are described (as Figure 2 shown):
[0060] (1) Construct an electrolyte solution system confined by flat plates: Construct a box with (L x = 4.43 nm, L y = 4.26 nm, 2L z = 10.0 nm), and randomly place 45 LiCl molecules and 2500 water molecules between two graphene flat plates composed of 720 C atoms located at z = 0 and 5 nm respectively (as Figure 3 shown).
[0061] (2) Process the AMOEBA force field parameters of the C atoms of the two flat plates.
[0062] (3) Molecular simulations were carried out using the Monte Carlo method with pressure control in the z - direction at a temperature of 298K and a pressure of 1atm to obtain a system with density equilibrium. The size of the system after equilibrium is (L x = 4.43nm, L y = 4.26nm, 2L z = 8.94nm).
[0063] (4) For the system obtained in step (3), molecular dynamics simulations without surface polarization effects were performed at 298K. A correction term for the current system needs to be added when calculating the atomic forces at each simulation step. After the simulation is completed, the simulation trajectory is processed to obtain the ensemble - averaged ion density distribution (as shown by the blue line in Figure 5 ).
[0064] (5) For each atom in the system obtained in step (3), an image atom symmetric about the L z = 0 flat plate was added, and the corresponding AMOEBA force field parameters were set for each image atom (as shown in Figure 4 ). Then, molecular dynamics simulations with conductor polarization effects were performed at 298K. After each molecular simulation step, each image atom needs to be moved to a position symmetric to the real atom. Finally, after the simulation is completed, the simulation trajectory is processed to obtain the ensemble - averaged ion density distribution (as shown by the green line in Figure 5 ).
[0065] In an embodiment of the present invention, a full - atom molecular dynamics simulation system for a double - plate confined system based on the AMOEBA force field is provided, which includes:
[0066] A processing module that constructs a double - plate confined simulation system and processes the force field parameters of the atoms constituting the flat plates to be applicable to this double - plate confined simulation system;
[0067] A density equilibrium module that, for the double - plate confined simulation system, performs pressure - control simulations using the Monte Carlo pressure bath along the normal direction of the conductor plane at a set temperature and pressure to achieve system density equilibrium;
[0068] An NVT simulation module without surface polarization that adds a flat - plate dipole correction term under the AMOEBA force field to the system after density equilibrium and performs NVT simulations without surface polarization at a set temperature; where the NVT simulation is a canonical ensemble simulation;
[0069] An NVT simulation module with conductor surface polarization effects that, in the system after density equilibrium, adds an image atom symmetric about the flat plate to each atom, sets the corresponding AMOEBA force field parameters for the image atom, and then performs NVT simulations with conductor surface polarization effects at a set temperature.
[0070] In the above embodiments, a double-plate confined simulation system is constructed, and the force field parameters of the atoms constituting the plates are processed, including:
[0071] A simulation box is constructed, the charges and masses of the plate atoms are set to 0, the bonding of the plate atoms is removed, and only the van der Waals interactions between the plate atoms and the atoms in the confined system are retained.
[0072] In the above embodiments, for the double-plate confined simulation system, pressure control simulation is performed along the normal direction of the conductor plane using Monte Carlo barostat at the set temperature and pressure to balance the system density, including:
[0073] Scale the size of the simulation box along the normal direction of the plate;
[0074] Move the plates and the molecules in the confined system in the system proportionally according to the change in the size of the box along the normal direction of the plate to obtain a double-plate confined simulation system with a new size;
[0075] Calculate the potential energy difference between the old and new systems, and use the Metropolis method to determine whether to accept this movement; if accepted, perform molecular dynamics simulation for a set number of steps to balance the new system; otherwise, return to the previous old system;
[0076] Repeat the above process until the currently set number of simulation steps is reached.
[0077] In the above embodiments, scaling the size of the simulation box along the normal direction of the plate specifically means: generating a random number R, setting the scaling size according to the random number R, and scaling the entire simulation box in the z direction by the set scaling size.
[0078] In the above embodiments, the plate dipole correction term under the AMOEBA force field is added to the system after density balancing, and NVT simulation without surface polarization is performed at the set temperature, including:
[0079] Calculate the dipole moment M of the system in the normal direction of the plate z ;
[0080] Add a correction force F to each example z,i After that, perform one step of molecular dynamics simulation, and determine whether the currently set number of simulation steps has been completed. If completed, the simulation of the system without surface polarization effect is completed; otherwise, recalculate system dipole moment in the direction normal to the plate M z 。
[0081] In the above embodiments, to correct the system without surface polarization, specifically, a correction force needs to be added to the force on each atom in the z direction at each molecular simulation step, and the correction force is:
[0082]
[0083] In the formula, F z,i is the correction force; q i is the charge of the atom; ∈0 is the vacuum permittivity; V is the total volume of the system; N is the total number of atoms in the system; z i is the z - coordinate of the atom, is the permanent dipole moment of the atom, is the induced dipole moment of the atom.
[0084] In the above - mentioned embodiment, in the system after density equilibrium, a mirror image atom symmetric about the flat plate is added to each atom, and corresponding AMOEBA force field parameters are set for the mirror image atom. Then, an NVT simulation with the conductor - surface polarization effect is performed at the set temperature, including:
[0085] Add a mirror image atom to each real atom, and sequentially set the force field parameters of each mirror image atom: set the mass of the mirror image atom to 0; remove all its bonding terms; the force field parameters of the van der Waals interaction are the same as those of its real atom; the charge is the same as that of its real atom but with the opposite sign, and the x and y components of the permanent dipole moment and the permanent quadrupole moment in the global coordinate system are partially opposite; the induced dipole parameters are the same as those of its real atom;
[0086] After each molecular simulation step is executed, move each mirror image atom in sequence to ensure that each mirror image atom is mirror - symmetric with its real atom about the flat plate at z = 0, and complete the simulation of the system with the conductor polarization effect.
[0087] The system provided in this embodiment is used to execute the above - mentioned method embodiments. For the specific process and detailed content, please refer to the above - mentioned embodiments and will not be elaborated here.
[0088] In an embodiment of the present invention, a computing device is provided. The computing device may be a terminal, which may include: a processor, a communications interface, a memory, a display screen, and an input device. Among them, the processor, the communications interface, and the memory complete their mutual communication through a communication bus. The processor is used to provide computing and control capabilities. The memory includes a non-volatile storage medium and an internal memory. The non-volatile storage medium stores an operating system and a computer program. When the computer program is executed by the processor, the methods in the above embodiments are implemented; the internal memory provides an environment for the operation of the operating system and the computer program in the non-volatile storage medium. The communications interface is used to communicate with an external terminal in a wired or wireless manner. The wireless manner can be implemented through WIFI, a carrier network, NFC (Near Field Communication), or other technologies. The display screen may be a liquid crystal display screen or an electronic ink display screen. The input device may be a touch layer covering the display screen, or a button, a trackball, or a touchpad provided on the housing of the computing device, or an external keyboard, touchpad, or mouse, etc. The processor can call the logical instructions in the memory.
[0089] In addition, when the logical instructions in the above-mentioned memory are implemented in the form of a software functional unit and sold or used as an independent product, they can be stored in a computer-readable storage medium. Based on such an understanding, the technical solution of the present invention, in essence, or the part that contributes to the prior art, or a part of this technical solution, can be embodied in the form of a software product. The computer software product is stored in a storage medium and includes several instructions for causing a computer device (which may be a personal computer, a server, or a network device, etc.) to execute all or part of the steps of the methods described in the various embodiments of the present invention. The aforementioned storage medium includes: USB flash drives, mobile hard disks, read-only memories (ROM, Read-Only Memory), random access memories (RAM, Random Access Memory), magnetic disks, or optical discs, etc., which can store program codes.
[0090] In an embodiment of the present invention, a computer program product is provided. The computer program product includes a computer program stored on a non-transitory computer-readable storage medium. The computer program includes program instructions. When the program instructions are executed by a computer, the computer can execute the methods provided in the above method embodiments.
[0091] In an embodiment of the present invention, a non-transitory computer-readable storage medium is provided. The non-transitory computer-readable storage medium stores server instructions. The computer instructions cause the computer to execute the methods provided in the above embodiments.
[0092] A computer-readable storage medium provided by the above embodiments has the same implementation principle and technical effects as the above method embodiments, and will not be elaborated here.
[0093] The present invention is described with reference to the flowcharts and / or block diagrams of methods, apparatuses (systems), and computer program products according to embodiments of the present invention. It should be understood that each process and / or block in the flowchart and / or block diagram, and the combination of processes and / or blocks in the flowchart and / or block diagram, can be implemented by computer program instructions. These computer program instructions can be provided to the processor of a general-purpose computer, a special-purpose computer, an embedded processor, or other programmable data processing devices to generate a machine, so that the instructions executed by the processor of the computer or other programmable data processing devices generate means for implementing the functions specified in one process Figure 1 one process or multiple processes and / or blocks Figure 1 or multiple blocks.
[0094] These computer program instructions can also be stored in a computer-readable memory that can direct a computer or other programmable data processing devices to work in a specific manner, so that the instructions stored in the computer-readable memory generate a manufactured article including instruction means, and the instruction means implements the functions specified in one process Figure 1 one process or multiple processes and / or blocks Figure 1 or multiple blocks.
[0095] These computer program instructions can also be loaded onto a computer or other programmable data processing devices, so that a series of operation steps are executed on the computer or other programmable devices to generate a computer-implemented process, and thus the instructions executed on the computer or other programmable devices provide steps for implementing the functions specified in one process Figure 1 one process or multiple processes and / or blocks Figure 1 or multiple blocks.
[0096] Finally, it should be noted that the above embodiments are only used to illustrate the technical solutions of the present invention, rather than to limit them; although the present invention has been described in detail with reference to the foregoing embodiments, those of ordinary skill in the art should understand that they can still modify the technical solutions recorded in the foregoing embodiments, or perform equivalent replacement; and these modifications or replacements do not cause the essence of the corresponding technical solutions to deviate from the technical partial technical features.
Claims
1. A full-atom molecular dynamics simulation method for a double-plate confined system based on the AMOEBA force field, characterized in that, Including: Construct a double - plate confined simulation system and process the force - field parameters of the atoms constituting the plates to be applicable to this double - plate confined simulation system; For the double - plate confined simulation system, perform pressure - control simulation along the normal direction of the conductor plane using Monte Carlo barostat at a set temperature and pressure to achieve system density equilibrium; Add the plate dipole correction term under the AMOEBA force field to the system after density equilibrium and perform NVT simulation without surface polarization at a set temperature; where, NVT simulation is canonical ensemble simulation; In the system after density equilibrium, add mirror atoms symmetric about the plate for each atom, set the corresponding AMOEBA force - field parameters for the mirror atoms, and then perform NVT simulation with conductor - surface polarization effect at a set temperature.
2. The all-atom molecular dynamics simulation method of the double-plate confined system based on the AMOEBA force field according to claim 1, wherein Construct a double - plate confined simulation system and process the force - field parameters of the atoms constituting the plates, including: Construct a simulation box, set the charges and masses of the plate atoms to 0, remove the bonding of the plate atoms, and only retain the van der Waals interaction between the plate atoms and the atoms of the confined system.
3. The all-atom molecular dynamics simulation method of the double-plate confined system based on the AMOEBA force field as described in claim 1, wherein, For the double - plate confined simulation system, perform pressure - control simulation along the normal direction of the conductor plane using Monte Carlo barostat at a set temperature and pressure to achieve system density equilibrium, including: Scale the size of the simulation box along the normal direction of the plate; Move the plates in the system and the molecules of the confined system proportionally according to the change in the size of the box along the normal direction of the plate to obtain a double - plate confined simulation system with the new size; Calculate the potential energy difference between the new and old systems, and use the Metropolis method to judge whether to accept this movement; if accepted, perform molecular dynamics simulation for a set number of steps to balance the new system; otherwise, return to the previous old system; Repeat the above process until the currently set number of simulation steps is reached.
4. The all-atom molecular dynamics simulation method for a double-plate confined system based on the AMOEBA force field according to claim 3, wherein, Scale the size of the simulation box along the normal direction of the plate. Specifically: generate a random number R, set the scaling size according to the random number R, and scale the entire simulation box in the z - direction by the set scaling size.
5. The all-atom molecular dynamics simulation method for a double-plate confined system based on the AMOEBA force field according to claim 1, characterized in that, Add the plate dipole correction term under the AMOEBA force field to the system after density equilibrium and perform NVT simulation without surface polarization at a set temperature, including: Dipole moment M of the computing system in the direction of the tablet normal z ; Add the correction force F to each example z,i After that, perform one step of molecular dynamics simulation and determine whether the currently set number of simulation steps has been completed. If it is completed, the simulation of the system without surface polarization effect is finished. Otherwise, recalculate the dipole moment M of the system in the direction normal to the flat plate z .
6. The all-atom molecular dynamics simulation method of the double-plate confined system based on the AMOEBA force field according to claim 5, characterized in that Correct the system without surface polarization. Specifically, at each molecular simulation step, add a correction force to the force on each atom in the z - direction. The correction force is: where, F z,i is the correction force; q i is the charge of the atom; ∈0 is the vacuum permittivity; V is the total volume of the system; N is the total number of atoms in the system; z i is the z-coordinate of the atom, is the permanent dipole moment of the atom, is the induced dipole moment of the atom.
7. The all-atom molecular dynamics simulation method of the double-plate confined system based on the AMOEBA force field according to claim 1, characterized in that In the system after density equilibrium, add mirror atoms symmetric about the plate for each atom, set the corresponding AMOEBA force - field parameters for the mirror atoms, and then perform NVT simulation with conductor - surface polarization effect at a set temperature, including: Add a mirror atom for each real atom, and sequentially set the force - field parameters of each mirror atom: set the mass of the mirror atom to 0; remove all its bonding terms; the force - field parameters of the van der Waals interaction are the same as those of its real atom; the charge is the same as that of its real atom but with the opposite sign, and the x and y components of the permanent dipole moment and permanent quadrupole moment in the global coordinate system are partially opposite; the induced dipole parameters are the same as those of its real atom; After each molecular simulation step, each mirror atom is moved in sequence to ensure that each mirror atom and its corresponding real atom are mirror symmetric about the flat plate at z = 0, thus completing the simulation of the system with conductor polarization effect.
8. A full-atom molecular dynamics simulation system for a double-plate confined system based on the AMOEBA force field, characterized in that, It includes: A processing module that constructs a double-flat-plate confined simulation system and processes the force field parameters of the atoms constituting the flat plates to be applicable to this double-flat-plate confined simulation system; A density equilibrium module that performs pressure control simulation along the normal direction of the conductor plane on the double-flat-plate confined simulation system at a set temperature and pressure using Monte Carlo pressure bath to achieve system density equilibrium; An NVT simulation module without surface polarization that adds a flat plate dipole correction term under the AMOEBA force field to the system after density equilibrium and performs NVT simulation without surface polarization at a set temperature; among them, NVT simulation is canonical ensemble simulation; An NVT simulation module with conductor surface polarization effect that adds mirror atoms symmetric about the flat plate to each atom in the system after density equilibrium, sets corresponding AMOEBA force field parameters for the mirror atoms, and then performs NVT simulation with conductor surface polarization effect at a set temperature.
9. A computer-readable storage medium storing one or more programs, characterized in that, The one or more programs include instructions that, when executed by a computing device, cause the computing device to execute any of the methods described in claims 1 to 7.
10. A computing device, characterized in that, It includes: One or more processors, a memory, and one or more programs, where the one or more programs are stored in the memory and configured to be executed by the one or more processors, and the one or more programs include instructions for executing any of the methods described in claims 1 to 7.