Method, system and equipment for limiting protein movement, storage medium and product

Abstract

The invention provides a method, system and device for limiting protein movement, a storage medium and a product, and the method comprises the steps: employing a distributed calculation strategy, dividing a calculation system into a plurality of calculation units, and each calculation unit is responsible for the analog calculation of a part of atoms of a processing molecular system; each calculation unit calculates the translation momentum and the angular momentum of the atom in charge of the calculation unit in parallel, and the calculation results are summarized into the global total momentum and the global total amount of the angular momentum; and calculating a centroid velocity, a centroid position and an angular velocity according to the obtained global total momentum and the obtained global total amount of the angular momentum, and broadcasting the centroid velocity, the centroid position and the angular velocity back to each calculation unit to carry out translation and rotation elimination on atoms which are responsible by the calculation units. According to the method, the efficiency of large-scale system simulation can be improved, the precision of long-time simulation is enhanced, and the parallel computing efficiency is improved.

Description

Technical Field

[0001] The present invention relates to the field of molecular dynamics simulation technology, and in particular to a method, system, device, storage medium and product for restricting protein movement. Background Art

[0002] Molecular dynamics simulation is a computational method based on Newton's laws of motion that can simulate the dynamic behavior of atoms and molecules on a time scale. By combining molecular dynamics simulation with protein structure prediction, valuable information about protein structure, conformational changes, and dynamic properties can be provided by simulating the dynamic behavior of proteins under physiological conditions. Molecular dynamics simulation is based on Newton's second law and simulates the motion trajectory of proteins on a time scale by solving the interaction forces between atoms. During the simulation process, it is necessary to consider parameters such as the atomic coordinates, velocity, and mass of the protein, and calculate the interaction forces between atoms based on the potential energy function. Through tens of thousands of iterative calculations, the motion trajectory and stable conformation of the protein can be obtained.

[0003] In molecular dynamics simulations, it is crucial to accurately describe the movement and interactions within molecules, while the overall translation and rotation (protein movement) of the molecular system often interferes with the acquisition of key information. Traditional methods usually deal with this problem at the software level, but with the improvement of computing power, the scale of molecular dynamics simulations is getting larger and larger, and the number of atoms involved in large molecular systems can reach millions. In this case, traditional software-level processing methods become extremely time-consuming and inefficient when eliminating translation and rotation, and computing time becomes the bottleneck of the simulation. At the same time, in long-time scale molecular dynamics simulations, even small numerical errors will accumulate over time, leading to significant deviations in the simulation results. Summary of the invention

[0004] In view of this, the present invention aims to propose a method, system, device, storage medium and product for restricting protein movement, which can improve the efficiency of large-scale system simulation, enhance the accuracy of long-term simulation, and improve the efficiency of parallel computing.

[0005] To achieve the above object, the technical solution of the present invention is achieved as follows:

[0006] A method for restricting protein movement, comprising:

[0007] S1. Use a distributed computing strategy to divide the computing system into multiple computing units, each of which is responsible for processing the simulation calculation of a part of the atoms in the molecular system;

[0008] S2, each computing unit calculates the translational momentum and angular momentum of the atoms it is responsible for in parallel, and the calculation results are summarized as the global total momentum and the global total angular momentum;

[0009] S3. According to the obtained global total momentum and global total angular momentum, the center of mass velocity, center of mass position, and angular velocity are calculated and broadcasted back to each computing unit to eliminate the translation and rotation of the atoms they are responsible for.

[0010] Furthermore, the division method of the computing system in step S1 includes: dividing into a three-dimensional grid structure, each grid unit includes a computing unit and a corresponding storage unit; each grid unit is directly connected to the surrounding grid units through a high-speed communication link; the edge grid units are connected to the opposite edge units to form periodic boundary conditions; all computing units execute computing tasks in parallel at the same time and the storage units support parallel reading and writing, allowing simultaneous computing and data access.

[0011] Furthermore, in step S2, the method for summarizing the calculation results includes:

[0012] The computing units within a certain range form a computing region, and one of the computing units is designated as a regional summary point of the computing region, and the regional summary point summarizes the calculation results of all computing units within the computing region;

[0013] A calculation unit is designated as a global management unit, and the summary calculation results of all regional summary points are transmitted to the global management unit to calculate the global total momentum and the global total amount of angular momentum.

[0014] Furthermore, the method for eliminating atomic translation in step S3 includes:

[0015] Dividing the global total momentum by the global total mass to obtain the center of mass velocity; the global total mass is the sum of the masses of all atoms in the molecular system;

[0016] Perform velocity correction on the atom, take the center-of-mass velocity as the correction value, subtract the correction value from the velocity of the atom to obtain the corrected velocity, and complete the elimination of translational motion.

[0017] Furthermore, the method for eliminating atomic rotation in step S3 includes:

[0018] Calculate the center of mass position and angular velocity through the global total of angular momentum;

[0019] To correct the velocity of the atom, first calculate the difference between the atomic position and the center of mass position, take the product of the difference and the angular velocity as the correction value, subtract the correction value from the atomic velocity to obtain the corrected velocity, and complete the elimination of rotation.

[0020] Another aspect of the present invention provides a system for restricting protein movement, comprising:

[0021] Partitioning modules: Using a distributed computing strategy, the computing system is divided into multiple computing units, each of which is responsible for processing the simulation calculation of a part of the atoms in the molecular system;

[0022] Calculation module: Each calculation unit calculates the translational momentum and angular momentum of the atoms it is responsible for in parallel, and the calculation results are summarized as the global total momentum and the global total angular momentum;

[0023] Elimination module: Based on the obtained global total momentum and global total angular momentum, the center of mass velocity, center of mass position, and angular velocity are calculated and broadcast back to each computing unit to eliminate the translation and rotation of the atoms they are responsible for.

[0024] Furthermore, the division modules include:

[0025] It is divided into a three-dimensional grid structure, each grid unit contains a computing unit and a corresponding storage unit; each grid unit is directly connected to the surrounding grid units through a high-speed communication link; the edge grid units are connected to the opposite edge units to form periodic boundary conditions; all computing units execute computing tasks in parallel and the storage units support parallel reading and writing, allowing simultaneous computing and data access.

[0026] Furthermore, the calculation module includes:

[0027] Regional summary submodule: the calculation units within a certain range form a calculation area, and one of the calculation units is designated as the regional summary point of the calculation area, and the regional summary point summarizes the calculation results of all the calculation units in the calculation area;

[0028] Global calculation module: designate a calculation unit as a global management unit, and the summary calculation results of all regional summary points are transmitted to the global management unit to calculate the global total momentum and the global total angular momentum.

[0029] Further, the elimination module includes a translation elimination submodule, and the translation elimination submodule includes:

[0030] Dividing the global total momentum by the global total mass to obtain the center of mass velocity; the global total mass is the sum of the masses of all atoms in the molecular system;

[0031] The velocity of the atom is corrected, the center-of-mass velocity is taken as the correction value, and the correction value is subtracted from the velocity of the atom to obtain the corrected velocity, thereby eliminating the atomic translation.

[0032] Further, the elimination module includes a rotation elimination submodule, and the rotation elimination submodule includes:

[0033] Calculate the center of mass position and angular velocity through the global total of angular momentum;

[0034] To correct the velocity of the atom, first calculate the difference between the atomic position and the center of mass position, take the product of the difference and the angular velocity as the correction value, subtract the correction value from the atomic velocity to obtain the corrected velocity, and complete the elimination of the atomic rotation.

[0035] On the other hand, the present invention also provides a device for limiting protein movement, comprising:

[0036] one or more processors;

[0037] A storage device for storing one or more programs;

[0038] When the one or more programs are executed by the one or more processors, the one or more processors implement the method for restricting protein movement as described above.

[0039] In another aspect, the present invention also provides a storage medium comprising computer executable instructions, which, when executed by a computer processor, are used to perform the method for restricting protein movement as described above.

[0040] On the other hand, an embodiment of the present invention further provides a computer program product, wherein the computer program product stores at least one program code, and the at least one program code is used to be executed by a processor to implement the above-mentioned method for restricting protein movement.

[0041] Compared with the prior art, the method, system, device, storage medium and product for restricting protein movement described in the present invention have the following advantages:

[0042] 1. The present invention adopts a distributed structure to simulate the molecular system and realizes a distributed and parallel processing mode, which can efficiently perform atomic data calculation, transmission aggregation and distribution, and avoid the channel congestion caused by the traversal transmission of the basic unit and other global basic units.

[0043] 2. The present invention adopts real-time data stream processing to realize the processing process of pipeline structure, which can calculate and eliminate translation and rotation while generating molecular coordinates and velocity data.

[0044] 3. The present invention configures a storage unit for each computing unit, so that the process quantities required for calculation can be stored using a large bit width, especially the quantities that need global accumulation. The order of magnitude fluctuation range is large according to the change of the simulation size, and the large bit width ensures the accuracy of the process quantities and result quantities.

[0045] 4. The present invention adopts a highly parallel processing mechanism, and the multi-level parallel architecture allows parallel computing at different scales, from a single computing unit to a computing region to a global computing. This design can make full use of the multi-level parallel architecture of modern supercomputers, such as multi-core CPUs, GPU clusters, etc.

[0046] 5. The present invention improves the numerical stability of molecular dynamics simulations. The hierarchical calculation and aggregation process adopted helps to reduce the accumulation of numerical errors, especially for large-scale molecular systems.

[0047] 6. The present invention is scalable, and the design of the solution takes into account the scalability from small clusters to large supercomputers. It can easily adapt to computing resources of different scales by adjusting the number of computing units and computing areas.

[0048] 7. The present invention adopts a flexible modular design, which makes it easy to integrate new algorithms or functional modules, which provides convenience for future expansion and improvement.

[0049] 8. The present invention provides an efficient, accurate and flexible solution for eliminating translation and rotation in large-scale molecular dynamics simulations by combining advanced parallel computing technology, sophisticated physical models and intelligent resource management strategies. It can not only improve the computing speed, but also handle more complex and larger-scale systems, providing a powerful computing tool for research in fields such as materials science and biophysics. BRIEF DESCRIPTION OF THE DRAWINGS

[0050] In order to more clearly illustrate the technical solutions in the embodiments of the present disclosure, the drawings required for use in the description of the embodiments will be briefly introduced below. Obviously, the drawings described below are only some embodiments of the present disclosure. For ordinary technicians in this field, other drawings can be obtained based on these drawings without paying any creative work.

[0051] Figure 1 This is a flow chart of the method for restricting protein movement according to Example 1 of the present invention;

[0052] Figure 2 This is a schematic diagram of the structure of the system for restricting protein movement according to Example 2 of the present invention;

[0053] Figure 3 This is a schematic diagram of the structure of the device for restricting protein movement described in Example 3 of the present invention. DETAILED DESCRIPTION

[0054] The specific embodiments described herein are only used to explain the present invention, but not to limit the present invention. It should also be noted that, for the convenience of description, only the parts related to the present invention, but not all structures, are shown in the drawings.

[0055] The design concept of the present invention mainly includes the following contents:

[0056] First, a distributed computing strategy is adopted to divide the entire system into multiple sub-units, each of which is responsible for processing the calculation of a part of the particles. This strategy makes full use of the parallel computing capabilities of special hardware.

[0057] Secondly, a phased calculation process is adopted. In the first phase, each unit calculates the translational momentum and angular momentum of the particles it is responsible for in parallel. In the second phase, the calculation results of the units in the specified area are summarized to the specified unit, and then these data are summarized to the global management unit to calculate the total momentum and angular momentum of the system. In the third phase, the calculation results are broadcast back to each unit to eliminate each atom.

[0058] The present invention is further described in detail below in conjunction with the accompanying drawings and embodiments.

[0059] Embodiment 1:

[0060] In Example 1, a method for limiting protein movement is proposed, such as Figure 1 As shown, including:

[0061] S1. Use a distributed computing strategy to divide the computing system into multiple computing units, each of which is responsible for processing the simulation calculation of a part of the atoms in the molecular system;

[0062] Among them, the distributed computing strategy provides a distributed, parallel processing method, which can efficiently aggregate and send data transmission, avoiding problems such as channel congestion caused by the transmission of all basic units and other global basic units. The specific method of dividing the computing units is as follows:

[0063] It is divided into a three-dimensional grid structure of X*Y*Z, and each grid point contains a computing unit and a storage unit corresponding to the computing unit. This structure of computing units and storage units helps to use a large bit width to store the process quantities that need to be calculated, especially the quantities that need global accumulation. The order of magnitude fluctuates widely depending on the changes in the simulation size, and the large bit width ensures the accuracy of the process quantities and result quantities.

[0064] The total number of computing units N_total = X*Y*Z. Each computing unit is directly connected to the computing units around it through high-speed communication links. The computing units at the edge of the three-dimensional grid structure may be connected to the computing units at the opposite edge, forming a periodic boundary condition. All computing units can execute computing tasks in parallel and the storage units support parallel reading and writing, allowing simultaneous computing and data access.

[0065] According to the above division structure, the system is initialized, which mainly includes the definition of atomic structure, the definition of computing unit structure, the definition of computing area, the definition of regional summary point, and the definition of global management unit.

[0066] Define the structure of the atom, including the atom ID, position r(x,y,z), velocity v(vx,vy,vz), mass m, whether it is restricted, etc.

[0067] Define the structure of the computational unit, including unit ID, atom list, unit range information, etc.

[0068] Define the calculation area structure, including area ID, calculation unit list, etc.;

[0069] Define regional summary point: The regional summary point is a specified calculation unit in the calculation area.

[0070] Define a global management unit: A global management unit is a specified computing unit in the computing system.

[0071] After the definition, the entire simulation space is divided into a three-dimensional grid structure, and each grid corresponds to a computing unit and a storage unit; then the computing units within a certain range area form a computing area (for example, the range area can be a three-dimensional grid of m*n*k, X is an integer multiple of m, Y is an integer multiple of n, and Z is an integer multiple of k). After all the computing units form multiple computing areas, a computing unit in the area is specified for each computing area as its area summary point; finally, a computing unit is specified as the global management unit of all computing areas.

[0072] Read all atomic information in the simulation space, including atomic position, velocity, mass, restriction marks, etc., and assign atoms to corresponding grids according to their positions. The computing unit corresponding to the grid is responsible for the simulation operations of the atoms in the grid, and the corresponding storage unit is responsible for storing the information of local atoms (i.e., all atoms in the grid).

[0073] S2, each computing unit calculates the translational momentum and angular momentum of the atoms it is responsible for in parallel, and the calculation results are summarized as the global total momentum and the global total angular momentum;

[0074] Specifically include:

[0075] 2.1 In order to eliminate translation, the translation momentum calculation is performed, including:

[0076] Calculate local momentum: read local atomic information from the corresponding storage unit and calculate the momentum of each atom inside: p i =m i *v i , where p irepresents the momentum of atom i, m i represents the mass of atom i, v i represents the velocity of atom i.

[0077] The total momentum P of this calculation unit is obtained by calculation unit =∑p i , total unit mass M local =∑m i .

[0078] Regional total momentum summary: Each calculation area (m*n*k) has a selected regional summary point, which summarizes the total momentum of all calculation units in the calculation area and then calculates the regional total momentum P region =∑P unit , the total mass of the region M region =∑M local .

[0079] Global total momentum calculation: According to the selected global management unit, the regional summary point of each calculation area transmits the regional total momentum of each calculation area to the global management unit to calculate the global total momentum P total =∑P region , and calculate the global total mass M total =∑M region .

[0080] 2.2 To eliminate the rotation, perform the calculation of angular momentum:

[0081] Calculate local angular momentum: Each computing unit reads local atomic information from the corresponding storage unit and calculates the momentum of each atom i inside, p i =m i *v i , where p i represents the momentum of atom i, m i represents the mass of atom i, v i Represents the velocity of atom i. Get the position r of atom i relative to the origin i , calculate the product of position and mass mr i =m i *r i , and the inertia tensor contribution: I i , angular momentum contribution: L i =r i *p i . Add up to get the total unit amount: P unit =∑p i MR unit =∑mr i ; L unit =∑L i ;I unit =∑Ii ,M unit =∑m i .

[0082] Angular momentum regional momentum summary: For each calculation area, the unit total of all calculation units in the area is transferred to the regional summary point, and the P of each calculation unit in the area is calculated. unit , MR unit ,I unit , L unit 、M unit The cumulative total: P region , MR region ,I region , L region 、M region .

[0083] Global total angular momentum summary: Accumulate P of all calculation areas in the global management unit region , MR region ,I region , L region 、M region , and get the global total P total , MR total ,I total , L total 、M total .

[0084] S3. According to the obtained global total momentum and global total angular momentum, the center of mass velocity, center of mass position, and angular velocity are calculated and broadcasted back to each computing unit to eliminate the translation and rotation of the atoms they are responsible for.

[0085] Specifically include:

[0086] 3.1 Eliminate translational motion:

[0087] Calculate the center of mass velocity based on the calculation results in step 2.1.

[0088] v cm =P total / M total ; where v cm represents the velocity of the center of mass;

[0089] The global snap-in will v cm Broadcast to all computing units, and in each computing unit, use the center of mass velocity as a correction value to correct the velocity of each atom. Represents the corrected speed. This correction can eliminate the effect of translation.

[0090] 3.2 Eliminate rotation:

[0091] According to the calculation results of step 2.2, calculate the center of mass position r cm =MR total / M total , center of mass velocity v cm =P total / M total , the inertia tensor I relative to the center of mass cm , the angular momentum L relative to the center of mass cm =r cm *P total Finally, solve the angular velocity ω=(I total -I cm ) -1 *(L total -L cm ).

[0092] The global management unit will be r cm and ω are broadcast to all computational units and are corrected in parallel in each computational unit as correction values. For each atom i: Represents the corrected speed. This correction eliminates the effect of rotation.

[0093] Regardless of eliminating translational motion, eliminating rotational motion, or eliminating translational motion and rotational motion, the corrected velocity is written back to the storage unit after elimination.

[0094] The elimination process implements pipeline processing, and the translation and rotation are calculated and eliminated while the atomic coordinates and velocity data are generated.

[0095] The method proposed in the first embodiment of the present invention provides an efficient, accurate and flexible solution for eliminating translation and rotation in large-scale molecular dynamics simulations by combining advanced parallel computing technology, sophisticated physical models and intelligent resource management strategies. It can not only improve the computing speed, but also handle more complex and larger-scale systems, providing a powerful computing tool for research in fields such as materials science and biophysics.

[0096] Embodiment 2:

[0097] Figure 2 Schematic diagram of the system structure for restricting protein movement provided by Example 2 of the present invention. Figure 2 As shown, the systems that restrict protein movement include:

[0098] Partitioning modules: Using a distributed computing strategy, the computing system is divided into multiple computing units, each of which is responsible for processing the simulation calculation of a part of the atoms in the molecular system;

[0099] Calculation module: Each calculation unit calculates the translational momentum and angular momentum of the atoms it is responsible for in parallel, and the calculation results are summarized as the global total momentum and the global total angular momentum;

[0100] Elimination module: Based on the obtained global total momentum and global total angular momentum, the center of mass velocity, center of mass position, and angular velocity are calculated and broadcast back to each computing unit to eliminate the translation and rotation of the atoms they are responsible for.

[0101] The division modules include:

[0102] It is divided into a three-dimensional grid structure, each grid unit contains a computing unit and a corresponding storage unit; each grid unit is directly connected to the surrounding grid units through a high-speed communication link; the edge grid units are connected to the opposite edge units to form periodic boundary conditions; all computing units execute computing tasks in parallel and the storage units support parallel reading and writing, allowing simultaneous computing and data access.

[0103] The calculation module specifically includes:

[0104] Regional summary submodule: the calculation units within a certain range form a calculation area, and one of the calculation units is designated as the regional summary point of the calculation area, and the regional summary point summarizes the calculation results of all the calculation units in the calculation area;

[0105] Global calculation module: designate a calculation unit as a global management unit, and transmit the summary calculation results of all regional summary points to the global management unit to calculate the global total momentum and the global total angular momentum.

[0106] The elimination module includes a translation elimination submodule and a rotation elimination submodule.

[0107] The translation elimination submodule comprises:

[0108] Dividing the global total momentum by the global total mass to obtain the center of mass velocity; the global total mass is the sum of the masses of all atoms in the molecular system;

[0109] The velocity of the atom is corrected, the center-of-mass velocity is taken as the correction value, and the correction value is subtracted from the velocity of the atom to obtain the corrected velocity, thereby eliminating the atomic translation.

[0110] The rotation elimination submodule comprises:

[0111] Calculate the center of mass position and angular velocity through the global total of angular momentum;

[0112] To correct the velocity of the atom, first calculate the difference between the atomic position and the center of mass position, take the product of the difference and the angular velocity as the correction value, subtract the correction value from the atomic velocity to obtain the corrected velocity, and complete the elimination of the atomic rotation.

[0113] The system for restricting protein movement provided by the embodiment of the present invention can execute the method for restricting protein movement provided by the first embodiment of the present invention, and has the corresponding functional modules for executing the method and the same beneficial effects as the method.

[0114] Embodiment three:

[0115] Figure 3 This is a schematic diagram of the structure of the device for restricting protein movement provided in Example 3 of the present invention. Figure 3 The device 1 shown is only an example and should not bring any limitation to the functions and scope of use of the embodiments of the present invention.

[0116] like Figure 3 As shown, the device 1 is in the form of a general-purpose computing device. The components of the device 1 may include, but are not limited to: one or more processors or processing units 3, a memory 8, and a bus 4 connecting different server components (including the memory 8 and the processing unit 3).

[0117] Bus 4 represents one or more of several types of bus structures, including a memory bus or memory controller, a peripheral bus, an accelerated graphics port, a processor or a local bus using any of a variety of bus structures. By way of example, these architectures include, but are not limited to, an Industry Standard Architecture (ISA) bus, a Micro Channel Architecture (MAC) bus, an Enhanced ISA bus, a Video Electronics Standards Association (VESA) local bus, and a Peripheral Component Interconnect (PCI) bus.

[0118] The device 1 typically includes a variety of computer server readable media. These media can be any available media that can be accessed by the device 1, including volatile and non-volatile media, removable and non-removable media.

[0119] The memory 8 may include computer server readable media in the form of volatile memory, such as random access memory (RAM) 9 and / or cache 10. The device 1 may further include other removable / non-removable, volatile / non-volatile computer server storage media. By way of example only, the storage system 11 may be used to read and write non-removable, non-volatile magnetic media ( Figure 3 not shown, usually called a "hard drive"). Although Figure 3Not shown in the figure, a disk drive for reading and writing to a removable non-volatile disk (e.g., a "floppy disk"), and an optical disk drive for reading and writing to a removable non-volatile optical disk (e.g., a CD-ROM, a DVD-ROM, or other optical media) may be provided. In these cases, each drive may be connected to the bus 4 via one or more data medium interfaces. The memory 8 may include at least one program product having a set (e.g., at least one) of program modules that are configured to perform the functions of the various embodiments of the present invention.

[0120] A program / utility 12 having a set (at least one) of program modules 13 may be stored, for example, in the memory 8, such program modules 13 including but not limited to operating servers, one or more application programs, other program modules, and program data, each of which or some combination may include the implementation of a network environment. The program modules 13 generally perform the functions and / or methods of the embodiments described herein.

[0121] The device 1 may also communicate with one or more external devices 2 (e.g., keyboards, pointing devices, displays 7, etc.), may communicate with one or more devices that enable a user to interact with the device 1, and / or may communicate with any device that enables the device 1 to communicate with one or more other computing devices (e.g., network cards, modems, etc.). Such communication may be performed via an input / output (I / O) interface 6. Furthermore, the device 1 may also communicate with one or more networks (e.g., local area networks (LANs), wide area networks (WANs), and / or public networks, such as the Internet) via a network adapter 5. As shown, the network adapter 5 communicates with other modules of the device 1 via a bus 4. It should be understood that, although not shown in the figure, other hardware and / or software modules may be used in the device 1, including but not limited to: microcode, device drivers, redundant processing units, external disk drive arrays, RAID servers, tape drives, and data backup storage servers, etc.

[0122] The processing unit 3 executes various functional applications and data processing by running the programs stored in the memory 8, such as implementing the method for restricting protein movement provided in the first embodiment of the present invention.

[0123] Embodiment 4:

[0124] Embodiment 4 of the present invention further provides a storage medium comprising computer executable instructions, which, when executed by a computer processor, are used to execute the method for restricting protein movement as provided in the above embodiment 1.

[0125] The computer storage medium of the embodiment of the present invention can adopt any combination of one or more computer-readable media. The computer-readable medium can be a computer-readable signal medium or a computer-readable storage medium. The computer-readable storage medium can be, for example, but not limited to, an electrical, magnetic, optical, electromagnetic, infrared, or semiconductor system, device or device, or any combination of the above. More specific examples (non-exhaustive list) of computer-readable storage media include: an electrical connection with one or more wires, a portable computer disk, a hard disk, a random access memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or flash memory), an optical fiber, a portable compact disk read-only memory (CD-ROM), an optical storage device, a magnetic storage device, or any suitable combination of the above. In this document, a computer-readable storage medium can be any tangible medium containing or storing a program, which can be used by an instruction execution system, device or device or used in combination with it.

[0126] Computer-readable signal media may include data signals propagated in baseband or as part of a carrier wave, which carry computer-readable program code. Such propagated data signals may take a variety of forms, including but not limited to electromagnetic signals, optical signals, or any suitable combination of the above. Computer-readable signal media may also be any computer-readable medium other than a computer-readable storage medium, which may send, propagate, or transmit a program for use by or in conjunction with an instruction execution system, apparatus, or device.

[0127] Program code embodied on a computer readable medium may be transmitted using any appropriate medium, including but not limited to wireless, wireline, optical fiber cable, RF, etc., or any suitable combination of the foregoing.

[0128] Computer program code for performing the operation of the present invention may be written in one or more programming languages ​​or a combination thereof, including object-oriented programming languages, such as Java, Smalltalk, C++, and conventional procedural programming languages, such as "C" or similar programming languages. The program code may be executed entirely on the user's computer, partially on the user's computer, as an independent software package, partially on the user's computer, partially on a remote computer, or entirely on a remote computer or device. In the case of a remote computer, the remote computer may be connected to the user's computer via any type of network, including a local area network (LAN) or a wide area network (WAN), or may be connected to an external computer (e.g., via the Internet using an Internet service provider).

[0129] Embodiment five:

[0130] An embodiment of the present invention provides a computer program product, which includes a computer program. The computer program can be stored on a non-transitory computer-readable storage medium. When the computer program is executed by a processor, the computer can execute the method for restricting protein movement provided in the above-mentioned embodiment 1.

[0131] Note that the above are only preferred embodiments of the present invention and the technical principles used. Those skilled in the art will understand that the present invention is not limited to the specific embodiments described herein, and that various obvious changes, readjustments and substitutions can be made by those skilled in the art without departing from the scope of protection of the present invention. Therefore, although the present invention has been described in more detail through the above embodiments, the present invention is not limited to the above embodiments, and may include more other equivalent embodiments without departing from the concept of the present invention, and the scope of the present invention is determined by the scope of the appended claims.

Claims

1. A method for restricting protein movement, characterized in that: include: S1. Use a distributed computing strategy to divide the computing system into multiple computing units, each of which is responsible for processing the simulation calculation of a part of the atoms in the molecular system; S2, each computing unit calculates the translational momentum and angular momentum of the atoms it is responsible for in parallel, and the calculation results are summarized as the global total momentum and the global total angular momentum; S3. Calculate the mass center velocity, mass center position, and angular velocity based on the obtained global total momentum and global total angular momentum, and broadcast them back to each computing unit to eliminate the translation and rotation of the atoms they are responsible for.

2. The method for restricting protein movement according to claim 1, characterized in that: The method for dividing the computing system in step S1 includes: dividing into a three-dimensional grid structure, each grid unit includes a computing unit and a corresponding storage unit; each grid unit is directly connected to the surrounding grid units through a high-speed communication link; the edge grid units are connected to the opposite edge units to form periodic boundary conditions; all computing units execute computing tasks in parallel at the same time and the storage units support parallel reading and writing, allowing simultaneous computing and data access.

3. The method for restricting protein movement according to claim 1, characterized in that: In step S2, the method for summarizing the calculation results includes: The computing units within a certain range form a computing region, and one of the computing units is designated as a regional summary point of the computing region, and the regional summary point summarizes the computing results of all computing units within the computing region; A calculation unit is designated as a global management unit, and the summary calculation results of all regional summary points are transmitted to the global management unit to calculate the global total momentum and the global total amount of angular momentum.

4. The method for restricting protein movement according to claim 1, characterized in that: The method for eliminating atomic translation in step S3 includes: Dividing the global total momentum by the global total mass to obtain the center of mass velocity; the global total mass is the sum of the masses of all atoms in the molecular system; Perform velocity correction on the atom, take the center-of-mass velocity as the correction value, subtract the correction value from the velocity of the atom to obtain the corrected velocity, and complete the elimination of translational motion.

5. The method for restricting protein movement according to claim 1, characterized in that: The method for eliminating atomic rotation in step S3 includes: Calculate the center of mass position and angular velocity through the global total of angular momentum; To correct the velocity of the atom, first calculate the difference between the atomic position and the center of mass position, take the product of the difference and the angular velocity as the correction value, subtract the correction value from the atomic velocity to obtain the corrected velocity, and complete the elimination of rotation.

6. A system for restricting protein movement, characterized in that include: Partitioning modules: Using a distributed computing strategy, the computing system is divided into multiple computing units, each of which is responsible for processing the simulation calculation of a part of the atoms in the molecular system; Calculation module: Each calculation unit calculates the translational momentum and angular momentum of the atoms it is responsible for in parallel, and the calculation results are summarized as the global total momentum and the global total angular momentum; Elimination module: Based on the obtained global total momentum and global total angular momentum, the center of mass velocity, center of mass position, and angular velocity are calculated and broadcast back to each computing unit to eliminate the translation and rotation of the atoms they are responsible for.

7. The system for restricting protein movement according to claim 6, characterized in that: The division modules include: It is divided into a three-dimensional grid structure, each grid unit contains a computing unit and a corresponding storage unit; each grid unit is directly connected to the surrounding grid units through a high-speed communication link; the edge grid units are connected to the opposite edge units to form periodic boundary conditions; all computing units execute computing tasks in parallel and the storage units support parallel reading and writing, allowing simultaneous computing and data access.

8. The system for restricting protein movement according to claim 6, characterized in that: The computing module includes: Regional summary submodule: the calculation units within a certain range form a calculation area, and one of the calculation units is designated as the regional summary point of the calculation area, and the regional summary point summarizes the calculation results of all the calculation units in the calculation area; Global calculation module: designate a calculation unit as a global management unit, and the summary calculation results of all regional summary points are transmitted to the global management unit to calculate the global total momentum and the global total angular momentum.

9. The system for restricting protein movement according to claim 6, characterized in that: The elimination module includes a translation elimination submodule, and the translation elimination submodule includes: Dividing the global total momentum by the global total mass to obtain the center of mass velocity; the global total mass is the sum of the masses of all atoms in the molecular system; The velocity of the atom is corrected, the center of mass velocity is used as the correction value, and the correction value is subtracted from the velocity of the atom to obtain the corrected velocity, thereby eliminating the atomic translation.

10. The system for restricting protein movement according to claim 6, characterized in that: The elimination module includes a rotation elimination submodule, and the rotation elimination submodule includes: Calculate the center of mass position and angular velocity through the global total of angular momentum; To correct the velocity of the atom, first calculate the difference between the atomic position and the center of mass position, take the product of the difference and the angular velocity as the correction value, subtract the correction value from the atomic velocity to obtain the corrected velocity, and complete the elimination of the atomic rotation.

11. A device for limiting protein movement, characterized in that include: one or more processors; A storage device for storing one or more programs; When the one or more programs are executed by the one or more processors, the one or more processors implement the method for restricting protein movement as described in any one of claims 1 to 5.

12. A storage medium containing computer executable instructions, characterized in that: The computer executable instructions are used to perform the method for restricting protein movement as described in any one of claims 1 to 5 when executed by a computer processor.

13. A computer program product, characterized in that The computer program product stores at least one program code, and the at least one program code is used to be executed by a processor to implement the method for restricting protein movement as described in any one of claims 1-5.

Images