Molecular dynamics simulation method and device, computer equipment and storage medium

Abstract

The embodiment of the invention provides a molecular dynamics simulation method, a molecular dynamics simulation device, computer equipment and a computer storage medium, and relates to the technical field of data processing. The method comprises the steps that an actual physical space is divided into a plurality of calculation unit areas in advance, and atomic information in different physical space areas in the actual physical space is distributed to the calculation unit areas corresponding to the physical space areas; for a target atom in each calculation unit area, when the position of the target atom in the first calculation unit area exceeds the boundary position of the first calculation unit area, the to-be-migrated direction of the target atom is determined; and migrating the target atoms in the first calculation unit area to the second calculation unit area based on the to-be-migrated direction. According to the method, the scale and efficiency of molecular dynamics simulation can be improved, and the data transmission quantity is reduced.

Description

Technical Field

[0001] The present application relates to the field of data processing technology, and in particular, to a molecular dynamics simulation method, a molecular dynamics simulation device, a computer device and a computer storage medium. Background Art

[0002] Molecular dynamics (MD) is a cutting-edge technology that combines mathematics, physics, chemistry, biology and other disciplines. Generally speaking, there are three methods for studying the structure and properties of molecular systems: experiments, theoretical research and simulations. Molecular dynamics simulation (MD simulation) is a molecular simulation method based on Newton's laws of motion, which is used to calculate the time-related properties of molecular systems. MD simulation can predict the position, velocity and kinetic energy of the branch system based on the position, velocity and kinetic energy of the current molecular system, thereby revealing the objective laws of molecular motion. However, with the continuous increase in the scale and complexity of the simulation system, the traditional molecular dynamics simulation method faces huge challenges in terms of computational efficiency and data processing when dealing with large-scale systems. Summary of the invention

[0003] The embodiments of the present application provide a molecular dynamics simulation method, a molecular dynamics simulation device, a computer device and a computer storage medium, thereby overcoming, at least to a certain extent, the technical problems of low computing efficiency and large data transmission volume due to the limitations and defects of related technologies.

[0004] A first aspect of an embodiment of the present application provides a molecular dynamics simulation method, the method comprising: pre-dividing the actual physical space into a plurality of computing unit regions, and allocating atomic information in different physical space regions in the actual physical space to computing unit regions corresponding to the physical space regions; for a target atom in each computing unit region, when the position of the target atom in a first computing unit region exceeds the boundary position of the first computing unit region, determining the direction in which the target atom is to be migrated; and migrating the target atom in the first computing unit region to a second computing unit region based on the direction in which the target atom is to be migrated.

[0005] According to a second aspect of an embodiment of the present application, a molecular dynamics simulation device is provided, which includes: a region division module for pre-dividing the actual physical space into a plurality of computing unit regions, and allocating atomic information in different physical space regions in the actual physical space to computing unit regions corresponding to the physical space regions; a direction determination module for determining the direction in which the target atom is to be migrated for a target atom in each computing unit region when the position of the target atom in a first computing unit region exceeds the boundary position of the first computing unit region; and an atom migration module for migrating the target atom in the first computing unit region to the second computing unit region based on the direction in which the target atom is to be migrated.

[0006] According to a third aspect of an embodiment of the present application, a computer device is provided, including a memory and a processor, wherein the memory stores a computer program, and when the processor executes the computer program, the steps of any of the above molecular dynamics simulation methods are implemented.

[0007] According to a fourth aspect of the embodiments of the present application, a computer-readable storage medium is provided, on which a computer program is stored. When the computer program is executed by a processor, the steps of the molecular dynamics simulation method as described above are implemented.

[0008] According to a fifth aspect of the embodiments of the present application, a computer program product is provided, including a computer program, which is executed by a processor to implement the steps of any one of the molecular dynamics simulation methods described above.

[0009] The technical solution of this application has the following beneficial effects:

[0010] Through this molecular dynamics simulation method, the actual physical space is divided into multiple calculation unit areas in advance, and the atomic information in different physical space areas in the actual physical space is allocated to the calculation unit area corresponding to the physical space area; for the target atom in each calculation unit area, when the position of the target atom in the first calculation unit area exceeds the boundary position of the first calculation unit area, the direction of the target atom to be migrated is determined; based on the direction to be migrated, the target atom in the first calculation unit area is migrated to the second calculation unit area. On the one hand, this method divides the continuous actual physical space into multiple discrete calculation unit areas to calculate the atomic migration data in parallel in multiple discrete calculation unit areas, which not only realizes the efficient use of computing resources and has excellent scalability, but also improves the computing efficiency and the speed of branch dynamics simulation. On the other hand, this method can greatly increase the scale of the system that can be simulated on the basis of improving parallel efficiency, thereby improving the scope of application of molecular dynamics simulation. BRIEF DESCRIPTION OF THE DRAWINGS

[0011] The drawings described herein are used to provide a further understanding of the present application and constitute a part of the present application. The illustrative embodiments of the present application and their descriptions are used to explain the present application and do not constitute an improper limitation on the present application. In the drawings:

[0012] Figure 1 An architecture diagram of a molecular dynamics simulation system provided for one embodiment of the present application;

[0013] Figure 2 A flow chart of a molecular dynamics simulation method provided for one embodiment of the present application;

[0014] Figure 3 A flow chart of a method for constructing a second data structure for atomic migration provided in one embodiment of the present application;

[0015] Figure 4 A schematic diagram of a second data structure provided for one embodiment of the present application;

[0016] Figure 5 A flow chart of a method for migrating complex molecules provided in one embodiment of the present application;

[0017] Figure 6 A schematic diagram of the structure of a molecular dynamics simulation device provided in one embodiment of the present application;

[0018] Figure 7 A schematic diagram of the computer device structure provided for one embodiment of the present application. DETAILED DESCRIPTION

[0019] Example embodiments will now be described more fully with reference to the accompanying drawings. However, example embodiments can be implemented in a variety of forms and should not be construed as being limited to the examples set forth herein; on the contrary, these embodiments are provided so that the present disclosure will be more comprehensive and complete, and the concepts of the example embodiments are fully conveyed to those skilled in the art. The described features, structures, or characteristics may be combined in one or more embodiments in any suitable manner. In the following description, many specific details are provided to provide a full understanding of the embodiments of the present disclosure. However, those skilled in the art will appreciate that the technical solutions of the present disclosure may be practiced while omitting one or more of the specific details, or other methods, components, devices, steps, etc. may be adopted. In other cases, known technical solutions are not shown or described in detail to avoid obscuring various aspects of the present disclosure.

[0020] In addition, the accompanying drawings are only schematic illustrations of the present disclosure and are not necessarily drawn to scale. The same reference numerals in the figures represent the same or similar parts, and their repeated description will be omitted. Some of the block diagrams shown in the accompanying drawings are functional entities and do not necessarily correspond to physically or logically independent entities. These functional entities can be implemented in software form, or implemented in one or more hardware modules or integrated circuits, or implemented in different networks and / or processor devices and / or microcontroller devices.

[0021] The flowcharts shown in the accompanying drawings are only exemplary and do not necessarily include all the steps. For example, some steps may be decomposed, while some steps may be combined or partially combined, so the actual execution order may change according to the actual situation.

[0022] In the relevant technical background, the methods for studying the structure and properties of molecular systems are divided into three categories: experiments, theoretical research, and simulations. Molecular dynamics simulation (MDS) is a molecular simulation method based on Newton's laws of motion. It mainly relies on computer technology to simulate the evolution of molecules and atomic systems over time to study molecular motion and interactions. That is, MD simulation can predict the position, velocity, and kinetic energy of the branch system based on the position, velocity, and kinetic energy of the current molecular system, thereby revealing the objective laws of molecular motion. Therefore, in modern scientific research, it has become one of the important tools for studying the dynamic behaviors of the microscopic world, such as material properties, biological processes, and chemical reactions.

[0023] However, with the continuous increase in the scale of simulation systems and the continuous improvement in the complexity of simulation systems, traditional mainstream molecular dynamics simulation methods, such as those based on single-core processors, use serial execution in the initialization and calculation stages of simulation tasks, resulting in widespread computational inefficiency in large-scale molecular dynamics simulation processes, making it impossible to fully utilize existing high-performance computing hardware resources, which in turn leads to the technical problem of low molecular dynamics simulation speed.

[0024] The exemplary embodiment of the present application takes the above problems into consideration and proposes a molecular dynamics simulation method, which divides the continuous actual physical space into multiple discrete computing unit areas to calculate the atomic migration data in parallel in multiple discrete computing unit areas, which not only realizes the efficient use of computing resources and has excellent scalability, but also improves the computing efficiency and the speed of branching dynamics simulation. In addition, based on the improvement of parallel efficiency, this method can also greatly increase the scale of the system that can be simulated, thereby increasing the scope of application of molecular dynamics simulation.

[0025] The following will be combined Figure 1, a molecular dynamics simulation method and device proposed in this application is applied to Figure 1 An embodiment of the system architecture of the exemplary application environment is described.

[0026] Figure 1 Schematic diagram of a molecular dynamics simulation system according to the exemplary embodiment is shown; Figure 1 As shown, it is a schematic diagram of an application scenario provided by an embodiment of the present application. In this scenario, a terminal device 101 and a server 102 may be included.

[0027] Among them, the terminal device 101 can be, for example, a mobile phone, a tablet computer (PAD), a laptop computer, a desktop computer, a smart TV, a smart car device, a smart wearable device, a smart TV, and an aircraft, etc., any device that involves the need for molecular dynamics simulation. The terminal device 101 can be installed with a target application, and the target application can have functions such as triggering molecular dynamics simulation. The application involved in the embodiment of the present disclosure can be a software client, or a client such as a web page or a small program. The server 102 is a server corresponding to the software or a web page, a small program, etc., and does not limit the specific type of the client.

[0028] The server 202 may be a background server of the target application, used to provide corresponding background services for it, such as molecular dynamics simulation services, etc. It may be an independent physical server, or a server cluster or distributed system composed of multiple physical servers, or a cloud server that provides basic cloud computing services such as cloud services, cloud databases, cloud computing, cloud functions, cloud storage, network services, cloud communications, middleware services, domain name services, security services, i.e., content delivery networks (CDNs), and big data and artificial intelligence platforms, but is not limited thereto.

[0029] In the embodiment of the present disclosure, the terminal device 101 and the server 102 can be directly or indirectly connected to each other through one or more networks 103. The network 103 can be a wired network or a wireless network. For example, the wireless network can be a mobile cellular network or a wireless fidelity (Wireless-Fidelity, WIFI) network. Of course, it can also be other possible networks, which are not limited in the embodiment of the present application. It should be noted that Figure 1 The figure is only an example. In fact, the number of terminal devices and servers is not limited and is not specifically limited in the embodiments of the present application.

[0030] It should be noted that when the molecular dynamics simulation method provided in the embodiment of the present application is executed by the server 102 or the terminal device 101 alone, the above-mentioned application scenario may also only include a single device of the server 102 or the terminal device 101, or the server 102 and the terminal device 101 may be considered to be the same device. Of course, in actual application, when the molecular dynamics simulation method provided in the embodiment of the present application is jointly executed by the server 102 and the terminal device 101, the server 102 and the terminal device 101 may also be the same device, that is, the server 102 and the terminal device 101 may be different functional modules of the same device, or virtual devices virtualized from the same physical device.

[0031] For example, in an exemplary embodiment, the target application is run by the terminal device 101, so that the user triggers a start instruction for executing the molecular dynamics simulation from the target application, and the server 102 can, upon receiving the start instruction,...

[0032] Below, in combination with the application scenarios described above, the method provided by the exemplary implementation of the present application is described with reference to the accompanying drawings. It should be noted that the above application scenarios are only shown to facilitate understanding of the spirit and principle of the present application, and the implementation of the present application is not limited in this respect. It should be noted that the following method can be executed by the above terminal device or server, or by the terminal device and the server together. Here, it is specifically shown by taking the execution of the terminal device or the server as an example.

[0033] See also Figure 2 As shown, Figure 2 A flow chart showing a molecular dynamics simulation method in this exemplary embodiment, which can be executed by a computer device, which can be Figure 1 The terminal device or server shown. Figure 2 The molecular dynamics simulation method provided by the embodiment of the present disclosure includes the following steps 201 to 203:

[0034] Step 201 , pre-dividing the actual physical space into a plurality of computing unit regions, and allocating the atomic information in different physical space regions in the actual physical space to the computing unit regions corresponding to the physical space regions.

[0035] Step 202 : for a target atom in each calculation unit region, when the position of the target atom in the first calculation unit region exceeds the boundary position of the first calculation unit region, determine the direction in which the target atom is to be migrated.

[0036] Step 203: Migrate the target atoms in the first computing unit region to the second computing unit region based on the direction to be migrated.

[0037] In the above Figure 2 In the technical solution provided in the embodiment, the actual physical space is divided into a plurality of calculation unit areas in advance, and the atomic information in different physical space areas in the actual physical space is allocated to the calculation unit area corresponding to the physical space area; for the target atom in each calculation unit area, when the position of the target atom in the first calculation unit area exceeds the boundary position of the first calculation unit area, the direction of the target atom to be migrated is determined; based on the direction to be migrated, the target atom in the first calculation unit area is migrated to the second calculation unit area. On the one hand, the method divides the continuous actual physical space into a plurality of discrete calculation unit areas, so as to calculate the data of atomic migration in parallel in a plurality of discrete calculation unit areas, which not only realizes the efficient utilization of computing resources and has excellent scalability, but also improves the computing efficiency and the speed of branch dynamics simulation. On the other hand, on the basis of improving the parallel efficiency, the method can also greatly increase the scale of the system that can be simulated, thereby improving the scope of application of molecular dynamics simulation.

[0038] The following will be combined with specific embodiments to Figure 2 The specific implementation methods of each step in the embodiment shown are described in detail:

[0039] In step 201, the actual physical space is pre-divided into a plurality of computing unit regions, and the atomic information in different physical space regions in the actual physical space is allocated to the computing unit regions corresponding to the physical space regions.

[0040] The actual physical space is the real physical space of the central processing unit (CPU) core / hard disk, which is usually a continuous physical memory area.

[0041] Exemplarily, the continuous actual physical space may be divided into a plurality of discrete computing unit areas, so that each computing unit area corresponds to a computing unit, and a computing unit corresponds to its own specific computing resources such as computing power and storage capacity.

[0042] In this embodiment, the method of dividing the actual physical space into multiple computing unit areas cleverly discretizes the macroscopic physical space to facilitate subsequent parallel calculations in multiple computing unit areas, thereby improving the overall computing efficiency of the system while ensuring the accuracy of atomic migration at the microscopic level.

[0043] When the actual physical space is pre-divided into multiple computing unit areas in step 201, in an optional embodiment of the present application, a three-dimensional interconnected device structure of M*N*K is constructed; the actual physical space is mapped onto the three-dimensional interconnected device structure to divide the actual physical space into computing unit areas corresponding to the M*N*K number of the three-dimensional interconnected device structure, and one computing unit area corresponds to one computing unit.

[0044] The three-dimensional interconnected device structure includes multiple interconnected sub-devices, and each interconnected sub-device corresponds to a computing unit, which includes the corresponding target computing power and target storage capacity. M, N, and K are the numbers of interconnected sub-devices included in the three different dimensions of the three-dimensional interconnected device structure.

[0045] For example, the system can pre-configure a three-dimensional interconnected device structure of M*N*K, each interconnected sub-device corresponds to a computing unit, and defines the computing power and storage capacity of each computing unit. Therefore, the three-dimensional interconnected device structure can also be composed of M*N*K independent computing units. Then, the actual physical space is mapped to the three-dimensional interconnected device structure, and the actual physical space can be divided into M*N*K discrete computing unit areas corresponding to the three-dimensional interconnected device structure, so that one computing unit area can correspond to one computing unit.

[0046] It should be explained that the computing power and storage capacity of the computing units corresponding to each interconnected sub-device in the initial state may be the same or different, and may be determined according to actual needs; and the topological structure of the three-dimensional interconnected device structure may be any three-dimensional structure, such as a star structure, a cross structure, a bus structure, a ring structure, a grid structure or other three-dimensional structures, and the embodiments of the present application do not impose any special restrictions on this.

[0047] In this embodiment, by constructing a three-dimensional interconnected device structure of M*N*K, the macroscopic physical space can be mapped into the three-dimensional structure, and at the same time, each divided computing unit area corresponds to a computing unit, so that in the subsequent molecular dynamics simulation process, parallel calculations can be performed simultaneously in multiple computing units, thereby improving the efficiency and speed of the molecular dynamics simulation.

[0048] In addition to the method of dividing the actual physical space through the above-mentioned embodiments, the actual physical space can also be divided directly, and a computing unit can be configured for each of the divided areas. The embodiments of the present application do not impose any special restrictions on this.

[0049] In addition to pre-dividing the actual physical space into a plurality of computing unit regions based on the above embodiment, atomic information in different physical space regions in the actual physical space may also be synchronously allocated to computing unit regions corresponding to the physical space regions.

[0050] For example, due to atomic movement, migration, etc., atoms are usually in different physical space regions in the actual physical space. Therefore, after the actual physical space is divided into multiple computing unit regions, different physical space regions are allocated to different computing unit regions, and correspondingly, atoms in different physical space regions will also be allocated to corresponding computing unit regions.

[0051] In an optional embodiment of the present application, after the atomic information in different physical space regions in the actual physical space is allocated to the computing unit regions corresponding to the physical space regions in the above steps, the first data structure needs to be initialized. That is, for each first computing unit region in the plurality of computing unit regions, a first data structure corresponding to the first computing unit region is created.

[0052] The first computing unit area is any one of the multiple computing unit areas; the first data structure includes one or more of the data structures of the first offset parameter and the second offset parameter.

[0053] Taking the first calculation unit region as calculation unit region A as an example, the first offset parameter may be an atom migration list (atom_migration_list), which is used to characterize the offset of atoms to be migrated in various directions in calculation unit region A within calculation unit region A; and the second offset parameter may be an offset list of atoms involved in bonding (bonded_migration_list), which is used to characterize the offset of Bond atoms (i.e. atoms involved in bonding) to be migrated in various directions in calculation unit region A among all atoms involved in bonding in the calculation unit region A. In the above atom_migration_list and bonded_migration_list, atoms to be migrated or Bond atoms to be migrated are usually characterized in the form of serial number identification.

[0054] Illustratively, after allocating the atomic information in different physical space regions in the actual physical space to the computing unit regions corresponding to the physical space regions in step 201, data structures such as atom_migration_list and bonded_migration_list can be created in each computing unit region to implement the data structure initialization process.

[0055] It should be noted that the created first data structures such as atom_migration_list and bonded_migration_list may be stored in a temporary address of the current computing unit area.

[0056] In step 202, for a target atom in each calculation unit region, when the position of the target atom in the first calculation unit region exceeds the boundary position of the first calculation unit region, the direction in which the target atom is to be migrated is determined.

[0057] The target atom is any atom in each computing unit region, that is, for all atoms in each computing unit region, it is necessary to determine whether the position in the current computing unit region exceeds the boundary position in the current computing unit region to determine whether to shift.

[0058] Exemplarily, all atoms in each computing unit area are traversed. For the sake of convenience, each target atom in the first computing unit area is taken as an example. According to the position of the target atom in the first computing unit area, it is determined whether it exceeds the boundary position of the first computing unit area. If it exceeds, it is necessary to perform atomic shift on the target atom and determine the direction to be shifted for performing the atomic shift; otherwise, if it does not exceed, it is determined that there is no need to shift the target atom.

[0059] Furthermore, after determining whether to perform atomic migration for all atoms in all computing unit regions one by one and determining the direction to be migrated when it is determined that atomic migration is required, it is necessary to collect statistics on the migration information in order to ensure normal progress of the migration.

[0060] In an optional embodiment of the present disclosure, the number of first atoms to be migrated out of the second computing unit area in each direction is determined, and the number of second atoms to be migrated into the second computing unit area is determined; the available storage capacity in the second computing unit area is determined based on the number of first atoms and the second number of atoms, so as to determine the number of atoms that can be migrated in based on the available storage capacity.

[0061] The available storage capacity may be free storage capacity, which may determine the number of atoms that can be migrated into the computing unit region. Generally, the larger the available storage capacity in a computing unit region, the larger the number of atoms that can be migrated into the computing unit region.

[0062] Exemplarily, after determining the direction in which all atoms are to be migrated, the number of first atoms to be migrated out and the number of second atoms to be migrated in can be counted for each computing unit area. This allows the storage capacity available during the migration process to be determined, allowing the computing unit area to reserve sufficient storage capacity to accommodate the atoms to be migrated in.

[0063] It should be noted that while counting the number of first atoms to be migrated out and the number of second atoms to be migrated in corresponding to each computing unit area, it is also necessary to update the first data structures corresponding to each computing unit area, namely, atom_migration_list and bonded_migration_list data structures.

[0064] In this embodiment, by counting the number of first atoms to be moved out and the number of second atoms to be moved in in a computing unit area, the available storage capacity in the computing unit area can be quickly determined, and sufficient storage capacity can be reserved to accommodate the atoms to be moved in.

[0065] In the step of determining the number of atoms that can be migrated in based on the available storage capacity in the above embodiment, an interrupt instruction is configured for the second computing unit area to start an interrupt and stop receiving atoms to be migrated when the available storage capacity in the second computing unit area is empty or less than the capacity threshold.

[0066] The interrupt instruction is used to start an interrupt when the available storage capacity in the second computing unit area is empty or less than the capacity threshold, so that the second computing unit area stops receiving atoms to be migrated so as to perform subsequent operations.

[0067] Furthermore, in order to ensure the orderliness and data consistency during the atomic migration process, the following embodiments may be combined for implementation:

[0068] Figure 3 A flowchart of a method for constructing a second data structure for atomic migration provided in one embodiment of the present application, referring to Figure 3 As shown, the method comprises the following steps 301-303:

[0069] Step 301: Create a second data structure corresponding to each computing unit area.

[0070] The second data structure at least includes the number of atoms in different orders in each computing unit area. For example, the second data structure can be represented by send_atom_num. Figure 4 The data structure of the above send_atom_num is described.

[0071] Figure 4 A schematic diagram of a second data structure provided by an embodiment of the present application, referring to Figure 4 As shown, the second data structure is composed of a storage address and corresponding storage information. Figure 4 It can be seen that the second data structure contains the number of Bond atoms with bonding relationships, the total number of atoms to be migrated, and the number of atoms of different orders (e.g. Figure 4The number of atoms at the 5th, 4th, 3rd, 2nd and 1st orders are represented in ).

[0072] Step 302: In response to the first computing unit region receiving the second data structure sent by other computing unit regions, determine the starting offset address of each order atom in the first computing unit region according to the second data structure corresponding to the other computing unit regions.

[0073] The other computing unit regions are computing unit regions other than the first computing unit region among the multiple computing unit regions.

[0074] Exemplarily, each computing unit area creates a corresponding second data structure; taking the first computing unit area as an example, it can send the second data structure (send_atom_num) created based on the first computing unit area to other adjacent computing unit areas, and also receive the second data structure created by the corresponding computing unit area from other computing unit areas. Based on this embodiment, information sharing of the second data structure in multiple computing device areas is achieved.

[0075] For example, assuming that the actual physical space is divided into 27 computing unit areas, and the 27 computing unit areas are in different directions, the system will create corresponding second data structures (send_atom_num1 to send_atom_num27) in computing unit areas 1 to 27 for the 27 computing unit areas. For any computing unit area 1, it is necessary to count the number of atoms that migrate to 27 directions (including its own direction) and send the second data structure 1 (send_atom_num1) created in computing unit area 1 to other computing unit areas in the adjacent 26 directions (for example, computing unit areas 2 to 27). In response to this, computing unit area A will also receive the second data structures (send_atom_num2 to send_atom_num27) created in computing unit areas 2 to 27 from the computing unit areas 2 to 27 in the adjacent 26 directions.

[0076] In response to the first computing unit region receiving the second data structure sent by other computing unit regions, the starting offset address of each order atom in the first computing unit region can be determined according to the second data structure corresponding to the other computing unit regions.

[0077] Exemplarily, the first computing unit area can count the number of atoms to be migrated into the first computing unit area and the placement offsets of atoms of each order based on the second data structure sent by other computing unit areas, thereby calculating the starting offset address of atoms of each order in the first computing unit area.

[0078] In order to facilitate determination of the starting offset address send_atom_offset of each order atom to be migrated in each direction (for example, migration in 27 directions respectively), three directions are taken as an example for description below.

[0079] Assume that a computing unit region receives a second data structure sent by other computing unit regions as shown in the following Table 1:

[0080] Table 1

[0081] First-order atomic number Second-order atomic number Third-order atomic number The fourth atomic number Number of fifth-order atoms Direction 0 1 2 0 4 1 Direction 1 2 2 1 3 1 Direction 2 0 1 4 1 1

[0082] Then, the relative placement offsets order_step and offset of atoms of each order can be calculated, as shown in Table 2:

[0083] Table 2

[0084] First level Second order Third level Fourth level Level 5 Direction 0 1 2 0 4 1 Direction 1 2 2 1 3 1 Direction 2 0 1 4 1 1 order_step 3 5 5 8 3 offset 0 3 8 13 21

[0085] Finally, by adding the offset in Table 2 to the placement offset, we can get the starting offset address send_atom_offset of each order atom, as shown in Table 3 below:

[0086] Table 3

[0087] First level Second order Third level Fourth level Level 5 Direction 0 0 3 8 13 21 Direction 1 1 5 8 17 22 Direction 2 3 7 9 20 23

[0088] Step 303: Send the starting offset addresses of atoms of each order in the first computing unit region to other computing unit regions.

[0089] Exemplarily, after determining the starting offset address of each order atom in the first computing unit area based on receiving the second data structure in other computing unit areas, the starting offset address of each order atom in the first computing unit area can be sent to other computing unit areas.

[0090] It should be noted that each computing unit area will execute the above steps 301-303. Therefore, for the first computing unit area, in addition to sending the starting offset addresses of each order atom in the first computing unit area to other computing unit areas, it also needs to receive the starting offset addresses of each order atom in each other computing unit area from other computing unit areas respectively, so as to realize data sharing.

[0091] In this embodiment, on the one hand, by determining the starting offset address of each order atom in each calculation unit area and sharing the data of the starting offset address of each order atom, the orderliness and consistency of atomic information in the atomic migration process can be ensured, and then through the data synchronization and checking steps in each calculation unit area, the consistency and reliability of data in a complex parallel environment are ensured, and the credibility of the simulation results is improved. On the other hand, by creating the first data structure, the second data structure, such as atom_migration_list and bonded_migration_list and send_atom_num, the data management and data access efficiency in the molecular dynamics simulation process are significantly improved.

[0092] In the above Figure 3 Based on the embodiment shown, the branch dynamic simulation process not only includes single atoms, but also may include molecular systems formed by complex multi-atomic groups. In an optional embodiment of the present disclosure, for complex molecular systems, in order to ensure the integrity of the molecular structure during the migration process, the following can be used: Figure 5 The embodiment shown.

[0093] Figure 5 A flow chart of a method for migrating complex molecules provided in one embodiment of the present application; Figure 5 As shown, the method may include the following steps 501 to 503:

[0094] Step 501: Receive the starting offset addresses of atoms of each order in other computing unit regions.

[0095] Step 502: Determine the target frame headers of atoms to be migrated in each direction in the first computing unit area according to the starting offset addresses of atoms of each order in other computing unit areas and the initial starting frame headers of other computing unit areas in each direction.

[0096] Step 503 , in response to sending the target frame header of the atoms to be migrated in each direction in the first computing unit area to the other computing unit areas in each direction, updating the covalent bond atom table of the other computing unit areas in each direction.

[0097] The covalent bond atom table includes one or more of the bonding task relationship and bonding task parameters between covalent bond atoms. The initial start frame header is a default frame header generated by initialization.

[0098] Exemplarily, after synchronizing the starting offset addresses of atoms of each order in all computing unit areas, for each computing unit area, the target frame headers of atoms to be migrated in each direction in the first computing unit area can be calculated based on the starting offset addresses returned by other computing unit areas in each direction and the initial starting frame headers of other computing unit areas in each direction.

[0099] The target frame header includes pillow information generated for the first data structure, namely, atom_migration_frame_head generated for the first offset parameter of a single atom, and bonded_migration_frame_head generated for the second offset parameter of a covalent bond atom.

[0100] It should be explained that the number of frame headers of each order can be determined according to the second data structure send_atom_num, and the frame headers are discretized according to the indexes in the first offset parameter atom_migration_list and the second offset parameter bonded_migration_list, thereby ensuring the same atomic order as in the original computing unit area before migration.

[0101] In addition, in addition to sending target frame headers of atoms to be migrated in the first computing unit area in various directions to other computing unit areas in various directions, the first computing unit area can also receive target frame headers of atoms to be migrated in various directions in other computing unit areas sent by other computing unit areas in various directions, thereby updating the covalent bond atom table stored in the first computing unit area.

[0102] Exemplarily, in the process of executing step 503, taking atom a as an example, its corresponding covalent bond atom table atom_table stores the relative unit offset and offset of atom b, which forms a bonding pair with a, relative to the computing unit area where atom a is located, so that the relative unit offset and offset can be used to read the target frame header of atom b, and the target frame header of atom a can also be read out at the same time, and the unit position information and offset in the target frame header can be maliciously used to calculate the relative positions of atoms a and b, and update the information about b in the covalent bond atom table atom_table of atom a.

[0103] In addition, it is also necessary to count the length of the covalent bond atom table to be migrated to ensure that there is enough storage space to receive the length of the covalent bond atom table to be migrated.

[0104] This process can ensure the integrity of complex molecular structures during migration, which is particularly important for simulating macromolecules and polymer systems. In addition, this embodiment supports flexible processing from single atoms to complex multi-atomic groups (i.e., molecular systems), adapting to the needs of various complex molecular systems, thereby providing strong support for multi-scale simulations.

[0105] Furthermore, since the computing resources of the system are limited, during the molecular dynamics simulation, there will inevitably be atoms or molecules migrating to the boundaries of the simulation. In order to overcome the limitations of limited computing resources and provide the possibility for studying large-scale systems, the limited computing resources can be used to simulate an infinite migration space based on the following method.

[0106] In an optional embodiment of the present disclosure, the first computing unit region is a computing unit region at a simulation boundary, and the third computing unit region is a computing unit region at another simulation boundary. When executing step 202 to determine the direction in which the target atom is to be migrated, in response to the position of the target atom in the first computing unit region exceeding the boundary position of the first computing unit region, the direction in which the target atom is to be migrated is determined to be the direction in which the boundary position of the third computing unit region is located, so as to migrate to the third computing unit region.

[0107] For example, for atoms beyond the simulation boundary, their new positions at the corresponding opposite simulation boundary can be calculated, so that the information of these atoms can be migrated to the corresponding third calculation unit area, thereby achieving a periodic boundary effect.

[0108] In this embodiment, the possibility of future hardware development is fully considered, so that it can easily adapt to larger-scale parallel computing devices and has relatively excellent scalability.

[0109] In step 203, target atoms in the first computing unit region are migrated to the second computing unit region based on the direction to be migrated.

[0110] After executing step 203, the first data structure in the first computing unit area after the atom migration can be updated, thereby ensuring the consistency and reliability of data in a complex parallel environment and improving the credibility of the simulation results.

[0111] In addition, after executing step 203, the covalent bond atom table after the atom migration needs to be updated to reflect the new bonding relationship after the atom migration in the calculation unit area after the migration.

[0112] Furthermore, in order to ensure the accuracy and reliability of branch dynamic simulation, it is also necessary to perform global information synchronization after completing all migration operations and perform consistency check on the total number of atoms to ensure that the total number of atoms remains unchanged, there is no duplication or loss of atoms, and the integrity of the atomic group structure is maintained.

[0113] In an optional embodiment of the present disclosure, in response to each atom in a plurality of computing unit regions completing migration, the total number of atoms in the plurality of computing unit regions is counted so that the total number of atoms after completing the migration is the same as the total number of atoms before the migration.

[0114] After executing the above atomic migration, the next round of molecular dynamics simulation tasks can be assigned to each computing unit according to the new atomic distribution, thereby optimizing the subsequent interaction calculations, resetting the relevant counters and flags, and preparing for the next time step simulation. The simulation results, such as atomic position, velocity, energy and other information, can also be output regularly.

[0115] In order to facilitate users to view, the real-time data during the execution of the molecular dynamics simulation task can also be visualized.

[0116] Through the above embodiments, the system is able to efficiently handle complex atomic migration while maintaining high calculation accuracy and data consistency, thereby providing researchers with the ability to explore complex molecular systems more deeply and accurately.

[0117] In an optional embodiment of the present application, if the actual physical space is a protein structure, the process of molecular dynamics simulation of the protein further includes restricting the position of the multi-protein structure, and the specific process is as follows:

[0118] Mapping each atomic data in the protein structure to be processed to each node unit in a pre-configured three-dimensional network structure; wherein each node unit includes at least one storage unit and at least one computing unit;

[0119] According to the preset multi-level parallel computing architecture, from small to large levels, the global center of mass mass and global center of mass coordinates of the protein structure to be processed are calculated in sequence in the three-dimensional network structure;

[0120] Calculate the restriction force of the calculation unit of the center point of the protein structure to be processed in the three-dimensional network structure according to the global center of mass coordinates and the initial center of mass coordinates;

[0121] According to a preset multi-level parallel computing architecture, from large to small levels, the restraining force is distributed to each atom in the protein structure to be processed to obtain the combined force of each atom;

[0122] The corresponding atomic positions are updated based on each of the combined forces. If the updated atomic positions exceed the set simulation space of the protein structure to be processed in the three-dimensional network structure, the atomic coordinates are adjusted to the preset positions in the set simulation space.

[0123] In an optional embodiment of the present application, mapping each atomic data in the protein structure to be processed to each node unit in a preconfigured three-dimensional network structure includes:

[0124] Acquiring structural data of the protein structure to be processed, and extracting the atomic coordinates and atomic mass of each atom in the structural data;

[0125] Constructing a set simulation space of the protein structure to be processed based on the structural data, and dividing the set simulation space into a plurality of subspaces;

[0126] The atomic coordinates and the atomic mass corresponding to each subspace in the set simulation space are mapped to each node unit in the three-dimensional network structure.

[0127] In an optional embodiment of the present application, the preset multi-level parallel computing architecture includes, from small to large, a single node unit, a computing cluster structure, and a central structure; wherein one computing cluster structure includes at least two node units, and one central structure includes at least two computing cluster structures.

[0128] In an optional embodiment of the present application, the global center of mass mass and global center of mass coordinates of the protein structure to be processed are calculated in sequence in the three-dimensional network structure from small to large levels according to the preset multi-level parallel computing architecture, including:

[0129] For each of the node units, calculating the sum of the first atomic masses of all atoms in the node unit and the first coordinate component in the local process;

[0130] For each of the computing cluster structures, calculating the second atomic masses of all atoms in each of the computing cluster structures and the second coordinate component in the cluster according to the first atomic masses of each of the node units in the computing cluster structure and the first coordinate component;

[0131] For the central structure, the global center of mass mass and the global center of mass coordinates of the protein structure to be processed are calculated according to the second atomic masses and the second coordinate components in each of the cluster structures in the central structure.

[0132] In an optional embodiment of the present application, the limiting force is distributed to each atom in the protein structure to be processed from large to small levels according to a preset multi-level parallel computing architecture to obtain the combined force of each atom, including:

[0133] Distributing the restraining force to the protein structure to be processed and to each of the calculation cluster structures according to the second atomic masses and ratios of all atoms in each of the calculation cluster structures;

[0134] Each of the computing cluster structures distributes the received cluster structure restriction force to each of the node units according to the first atomic masses and proportions of all atoms in each of the node units;

[0135] Each of the node units distributes the received unit limiting force to each atom to obtain the resultant force of each atom.

[0136] In an optional embodiment of the present application, the method further includes:

[0137] For each atom in each of the node units, the atom is updated based on each resultant force to obtain updated atomic coordinates;

[0138] Determine whether the updated atomic coordinates are in the current node unit, and if the updated atomic coordinates exceed the current node unit, determine the new node unit to which the atom belongs according to the updated atomic coordinates;

[0139] The atoms and the atomic data corresponding to the atoms are transferred to the new node unit.

[0140] In an optional embodiment of the present application, the updating of the corresponding atomic positions based on each of the combined forces, if the updated atomic positions exceed the set simulation space of the protein structure to be processed in the three-dimensional network structure, adjusting the atomic coordinates to a preset position in the set simulation space, comprises:

[0141] Determining whether the updated atomic coordinates exceed the set simulation space;

[0142] If the updated atomic coordinates exceed the set simulation space, the atomic coordinates are adjusted to the nearest node unit in the set simulation space according to the updated atomic coordinates and the boundary data of the set simulation space.

[0143] It should be understood that, although the various steps in the flow chart are displayed in sequence according to the indication of the arrows, these steps are not necessarily executed in sequence according to the order indicated by the arrows. Unless there is a clear description in this article, the execution of these steps is not strictly limited in order, and these steps can be executed in other orders. Moreover, at least a portion of the steps in the figure may include multiple sub-steps or multiple stages, and these sub-steps or stages are not necessarily executed at the same time, but can be executed at different times, and the execution order of these sub-steps or stages is not necessarily to be carried out in sequence, but can be executed in turn or alternately with other steps or at least a portion of the sub-steps or stages of other steps.

[0144] To implement the molecular dynamics simulation method described above, see Figure 6An embodiment of the present application provides a molecular dynamics simulation device, and the molecular dynamics simulation device 600 may include: a region division module 601, a direction determination module 602 and an atomic migration module 603.

[0145] The region division module 601 is used to divide the actual physical space into a plurality of computing unit regions in advance, and to distribute the atomic information in different physical space regions in the actual physical space to the computing unit regions corresponding to the physical space regions;

[0146] A direction determination module 602 is used to determine, for a target atom in each calculation unit region, a direction in which the target atom is to be migrated when the position of the target atom in the first calculation unit region exceeds the boundary position of the first calculation unit region;

[0147] The atom migration module 603 is used to migrate the target atoms in the first computing unit area to the second computing unit area based on the direction to be migrated.

[0148] In an optional embodiment of the present disclosure, the region division module 601 is used to construct an M*N*K three-dimensional interconnected device structure, which includes multiple interconnected sub-devices, and each interconnected sub-device corresponds to a computing unit; the actual physical space is mapped to the three-dimensional interconnected device structure to divide the actual physical space into M*N*K computing unit regions corresponding to the three-dimensional interconnected device structure, and each computing unit region corresponds to a computing unit.

[0149] In an optional embodiment of the present disclosure, the device may also include a data creation module and an update module, the data creation module is used to create a first data structure corresponding to each first computing unit area among multiple computing unit areas, the first data structure includes one or more data structures of first offset parameters and second offset parameters; the first offset parameter represents the offset of atoms to be migrated in all directions in the first computing unit area within the first computing unit area, and the second offset parameter represents the offset of covalent bond atoms to be migrated in all directions in the first computing unit area among all covalent bond atoms in the first computing unit area; the update module is used to update the first data structure in the first computing unit area after the atom migration.

[0150] In an optional embodiment of the present disclosure, the device may also include a determination module, which is used to determine the number of first atoms to be migrated out of the second computing unit area in each direction, and determine the number of second atoms to be migrated into the second computing unit area; the determination module can also be used to determine the available storage capacity in the second computing unit area based on the number of first atoms and the number of second atoms, so as to determine the number of atoms that can be migrated in based on the available storage capacity.

[0151] In an optional embodiment of the present disclosure, the determination module may also be used to configure an interrupt instruction for the second computing unit area, so as to initiate an interrupt and stop receiving atoms to be migrated when the available storage capacity in the second computing unit area is empty or less than a capacity threshold.

[0152] In an optional embodiment of the present disclosure, the device may also include an information sending module, and the data creation module may also be used to create a second data structure corresponding to each computing unit area, the second data structure at least including the number of atoms at different orders in each computing unit area; the determination module may also be used to determine the starting offset address of atoms of each order in the first computing unit area in response to the first computing unit area receiving the second data structure sent by other computing unit areas, according to the second data structure corresponding to the other computing unit areas; the information sending module is used to send the starting offset address of atoms of each order in the first computing unit area to other computing unit areas, and the other computing unit areas are computing unit areas among multiple computing unit areas except the first computing unit area.

[0153] In an optional embodiment of the present disclosure, the device may also include an information receiving module, which is used to receive the starting offset addresses of atoms of each order in other computing unit areas; the determination module is also used to determine the target frame headers of atoms to be migrated in each direction in the first computing unit area based on the starting offset addresses of atoms of each order in other computing unit areas and the initial starting frame headers of other computing unit areas in each direction; the update module is also used to update the covalent bond atom table of other computing unit areas in each direction in response to sending the target frame headers of atoms to be migrated in each direction in the first computing unit area to other computing unit areas in each direction, wherein the covalent bond atom table includes one or more of the bonding task relationships and bonding task parameters between covalent bond atoms.

[0154] In an optional embodiment of the present disclosure, the first computing unit area is a computing unit area at a simulation boundary, and the third computing unit area is a computing unit area at another simulation boundary. The direction determination module 602 is specifically used to determine the direction of the target atom to be migrated as the direction of the boundary position of the third computing unit area in response to the position of the target atom in the first computing unit area exceeding the boundary position of the first computing unit area, so as to migrate to the third computing unit area.

[0155] In an optional embodiment of the present disclosure, the determination module is further used to determine the total number of atoms in the multiple computing unit areas in response to the completion of migration of each atom in the multiple computing unit areas, so as to determine that the total number of atoms after the completion of migration is the same as the total number of atoms before the migration.

[0156] The specific definition of the molecular dynamics simulation device can be found in the above definition of the molecular dynamics simulation method, which will not be repeated here. Each module in the molecular dynamics simulation device can be implemented in whole or in part by software, hardware and a combination thereof. Each of the modules can be embedded in or independent of a processor in a computer device in the form of hardware, or can be stored in a memory in a computer device in the form of software, so that the processor can call and execute operations corresponding to each of the modules above.

[0157] In one embodiment, a computer device is provided, the internal structure diagram of which can be as follows: Figure 7 As shown. The computer device includes a processor, a memory, a network interface and a database connected via a system bus. Among them, the processor of the computer device is used to provide computing and control capabilities. The memory of the computer device includes a non-volatile storage medium and an internal memory. The non-volatile storage medium stores an operating system, a computer program and a database. The internal memory provides an environment for the operation of the operating system and the computer program in the non-volatile storage medium. The database of the computer device is used to store data. The network interface of the computer device is used to communicate with an external terminal via a network connection. When the computer program is executed by the processor, a molecular dynamics simulation method as described above is implemented. It includes: a memory and a processor, the memory stores a computer program, and when the processor executes the computer program, any step in the molecular dynamics simulation method as described above is implemented.

[0158] In one embodiment, a computer-readable storage medium is provided, on which a computer program is stored. When the computer program is executed by a processor, any step in the above molecular dynamics simulation method can be implemented.

[0159] Those skilled in the art will appreciate that the embodiments of the present application may be provided as methods, systems, or computer program products. Therefore, the present application may adopt the form of a complete hardware embodiment, a complete software embodiment, or an embodiment in combination with software and hardware. Moreover, the present application may adopt the form of a computer program product implemented in one or more computer-usable storage media (including but not limited to disk storage, CD-ROM, optical storage, etc.) that include computer-usable program code.

[0160] The present application is described with reference to the flowcharts and / or block diagrams of the methods, devices (systems), and computer program products according to the embodiments of the present application. It should be understood that each process and / or box in the flowchart and / or block diagram, as well as the combination of the processes and / or boxes in the flowchart and / or block diagram, can be implemented by computer program instructions. These computer program instructions can be provided to a processor of a general-purpose computer, a special-purpose computer, an embedded processor, or other programmable data processing device to generate a machine, so that the instructions executed by the processor of the computer or other programmable data processing device generate instructions for implementing the processes in the flowchart and / or block diagram. Figure 1 A process or multiple processes and / or boxes Figure 1 A device that provides the functions specified in a block or multiple blocks.

[0161] These computer program instructions may also be stored in a computer-readable memory capable of directing a computer or other programmable data processing device to operate in a specific manner, so that the instructions stored in the computer-readable memory produce an article of manufacture comprising an instruction device, which implements the process Figure 1 A process or multiple processes and / or boxes Figure 1 A function specified in one or more boxes.

[0162] These computer program instructions can also be loaded onto a computer or other programmable data processing device so that a series of operating steps are executed on the computer or other programmable device to produce a computer-implemented process, thereby providing instructions for implementing the process. Figure 1 A process or multiple processes and / or boxes Figure 1 A step that specifies a function in one or more boxes.

[0163] Although the preferred embodiments of the present application have been described, those skilled in the art may make other changes and modifications to these embodiments once they have learned the basic creative concept. Therefore, the appended claims are intended to be interpreted as including the preferred embodiments and all changes and modifications falling within the scope of the present application.

[0164] Obviously, those skilled in the art can make various changes and modifications to the present application without departing from the spirit and scope of the present application. Thus, if these modifications and variations of the present application fall within the scope of the claims of the present application and their equivalents, the present application is also intended to include these modifications and variations.

Claims

1. A molecular dynamics simulation method, characterized in that: include: Dividing the actual physical space into a plurality of computing unit regions in advance, and allocating the atomic information in different physical space regions in the actual physical space to the computing unit regions corresponding to the physical space regions; For a target atom in each calculation unit region, when the position of the target atom in the first calculation unit region exceeds the boundary position of the first calculation unit region, determining the direction in which the target atom is to be migrated; Based on the direction to be migrated, the target atoms in the first computing unit region are migrated to the second computing unit region.

2. The method according to claim 1, characterized in that The actual physical space is divided into a plurality of computing unit areas in advance, including: Constructing a three-dimensional interconnected device structure of M*N*K, wherein the three-dimensional interconnected device structure includes a plurality of interconnected sub-devices, and each of the interconnected sub-devices corresponds to a computing unit; The actual physical space is mapped onto the three-dimensional interconnected device structure to divide the actual physical space into M*N*K number of computing unit areas corresponding to the three-dimensional interconnected device structure, and each of the computing unit areas corresponds to a computing unit.

3. The method according to claim 1, characterized in that After allocating the atomic information in different physical space regions in the actual physical space to the computing unit regions corresponding to the physical space regions, the method further includes: For each first computing unit region among the multiple computing unit regions, a first data structure corresponding to the first computing unit region is created, wherein the first data structure includes one or more data structures of a first offset parameter and a second offset parameter; the first offset parameter represents the offset of atoms to be migrated in various directions in the first computing unit region within the first computing unit region, and the second offset parameter represents the offset of covalent bond atoms to be migrated in various directions in the first computing unit region among all covalent bond atoms in the first computing unit region; Wherein, after migrating the atomic information of the target atom in the first computing unit region to the second computing unit region based on the direction to be migrated, the method further includes: A first data structure in the first computing unit region after the atomic migration is updated.

4. The method according to claim 1, characterized in that: After determining the direction in which the target atom is to be migrated, the method further comprises: Determine the number of first atoms to be migrated out of the second computing unit area in each direction, and determine the number of second atoms to be migrated into the second computing unit area; The available storage capacity in the second calculation unit area is determined according to the first atomic number and the second atomic number, so as to determine the number of atoms that can be migrated based on the available storage capacity.

5. The method according to claim 1 or 3, characterized in that: The method further comprises: Creating a second data structure corresponding to each computing unit region, wherein the second data structure at least includes the number of atoms at different orders in each computing unit region; In response to the first computing unit region receiving a second data structure sent by other computing unit regions, determining a starting offset address of each order atom in the first computing unit region according to the second data structure corresponding to the other computing unit regions; The starting offset addresses of atoms of each order in the first computing unit region are sent to the other computing unit regions, where the other computing unit regions are computing unit regions other than the first computing unit region in the plurality of computing unit regions.

6. The method according to claim 5, characterized in that The method further comprises: receiving the starting offset addresses of atoms of each order in the other computing unit regions; Determine the target frame headers of atoms to be migrated in each direction in the first computing unit area according to the starting offset addresses of atoms of each order in the other computing unit areas and the initial starting frame headers of other computing unit areas in each direction; In response to sending the target frame header of the atoms to be migrated in each direction in the first computing unit area to other computing unit areas in each direction, the covalent bond atom table of the other computing unit areas in each direction is updated, and the covalent bond atom table contains one or more of the bonding task relationships and bonding task parameters between the covalent bond atoms.

7. The method according to claim 1, characterized in that The first calculation unit region is a calculation unit region at a simulation boundary, the third calculation unit region is a calculation unit region at another simulation boundary, and the determining of the direction in which the target atom is to be migrated includes: In response to the position of the target atom in the first computing unit region exceeding the boundary position of the first computing unit region, the target atom is determined to migrate in a direction of the boundary position of the third computing unit region to migrate to the third computing unit region.

8. A molecular dynamics simulation device, characterized in that: include: A region division module, used to divide the actual physical space into a plurality of computing unit regions in advance, and to distribute the atomic information in different physical space regions in the actual physical space to the computing unit regions corresponding to the physical space regions; A direction determination module, for determining, for a target atom in each calculation unit region, a direction in which the target atom is to be migrated when the position of the target atom in the first calculation unit region exceeds the boundary position of the first calculation unit region; An atom migration module is used to migrate the target atoms in the first computing unit area to the second computing unit area based on the direction to be migrated.

9. A computer device comprising: The method comprises a memory and a processor, wherein the memory stores a computer program, and wherein the processor implements the steps of the molecular dynamics simulation method according to any one of claims 1 to 7 when executing the computer program.

10. A computer-readable storage medium having a computer program stored thereon, characterized in that: When the computer program is executed by a processor, the steps of the molecular dynamics simulation method according to any one of claims 1 to 7 are implemented.

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