Molecular system processing method and device related to molecular dynamics simulation

Abstract

The invention discloses a molecular system processing method and device related to molecular dynamics simulation, and the method comprises the steps: constructing a to-be-simulated molecular system through a Hierachy structure, reconstructing the Hierachy structure to obtain a balance tree Hierachy structure, carrying out the data updating of each basic element in a space unit of the balance tree Hierachy structure, and carrying out the data updating of the to-be-simulated molecular system through the data updating of each basic element in the space unit of the balance tree Hierachy structure. According to the method, data iteration is carried out on other space units at the same time until the top layer of the Hierarchy structure of the balance tree is completely updated, and the Hierarchy hierarchical structure and the actual molecular data file are connected through the index, so that the content of the unit or the space unit needing to be loaded is quickly found, the capacity of quick positioning is provided, and the operation efficiency is well improved.

Description

TECHNICAL FIELD

[0001] The present application relates to computer chemistry and computer biology technology, in particular to a method and device for processing a molecular system in a molecular dynamics simulation. BACKGROUND

[0002] Molecular dynamics (MD) has many application directions in the field of biomedical research and development, material science. Traditional experimental methods are difficult to observe the dynamic changes of complex biological macromolecules such as proteins, nucleic acids, etc. at the atomic or molecular level in real time. The molecular dynamics simulation device can provide detailed molecular trajectory and interaction information to help understand the relationship between structure and function.

[0003] With the rapid development of computer hardware technology, the operation speed of the processor, the performance and capacity of the storage device have been greatly improved, making it possible to process large-scale molecular dynamics simulation containing tens of thousands of atoms, providing a strong computing basis for the development of molecular dynamics simulation devices. SUMMARY

[0004] The present application overcomes the above-mentioned shortcomings of the prior art and provides a method and device for processing a molecular system in a molecular dynamics simulation, which can improve the operation efficiency.

[0005] The first aspect of the present application provides a method for processing a molecular system in a molecular dynamics simulation, comprising the following steps:

[0006] S1. Constructing a molecular system to be simulated using a hierarchy structure; wherein the top layer of the hierarchy structure includes all information of the molecular system to be simulated composed of one or more units; the bottom layer of the hierarchy structure includes information of basic elements determined according to simulation accuracy; between the top layer and the bottom layer of the hierarchy structure, there are one or more intermediate layers decomposed according to the chemical structure of the molecular system to be simulated, each intermediate layer including one or more units;

[0007] S2. Reconstructing the hierarchy structure to obtain a balanced tree hierarchy structure, the balanced tree hierarchy structure including the top layer of the hierarchy structure and one or more spatial units; wherein each spatial unit includes one or more basic elements, and the distance between the basic elements is within a predetermined range; an index is established between each unit or spatial unit and the storage location of the corresponding basic element;

[0008] S3. In the unit of space element, each basic element in the space element as the current target basic element, after the target element region reaches the balance state, respectively calculate the force of each basic element in the balance tree Hierarchy structure on the current target basic element and accumulate, while recording and saving the molecular motion process of the basic element from unbalanced state to balanced state in a period of time;

[0009] S4. According to the accumulated force, obtain the state information of the current target basic element, respectively calculate the force of each basic element in the balance tree Hierarchy structure on the current target basic element and accumulate, until all basic elements of the balance tree Hierarchy structure are traversed.

[0010] S5. Determine whether the end condition set in advance is met, if the end condition is met, end; if the end condition is not met, return to the step of respectively calculating the force of each basic element in the balance tree Hierarchy structure on the current target basic element and accumulating.

[0011] Wherein, the step S2 described the reconstruction of the Hierarchy structure, comprising:

[0012] S21. Reconstruct the Hierarchy structure using quadtree or region tree, including: defining the node class of quadtree or region tree, creating a class containing child nodes and node data.

[0013] S22. Extract all basic elements from the constructed Hierarchy structure; according to the distance between the basic elements, the basic elements with distance in the preset range are divided in the one or more space elements, to obtain the balance tree Hierarchy structure composed of space elements and root node of the Hierarchy structure.

[0014] In an exemplary example, further comprising: uniformly distributing all extracted basic elements in the space element corresponding to the child node by dynamic adjustment.

[0015] Wherein, the step S3 described the calculation of the force of each basic element in the balance tree Hierarchy structure on the current target basic element and accumulation, comprising:

[0016] S31. In the space element where the current target basic element is located, when the target element reaches the balance state, record the state information of the target element at this time, respectively calculate the force of each basic element on the current target basic element, and accumulate the obtained force to obtain the first accumulated force.

[0017] S32. Calculate the force of each basic element in other space units on the current target basic element respectively, and accumulate the obtained forces to obtain a second accumulated force in the other space units where the current target basic element is located.

[0018] S33. Accumulate the first accumulated force and the second accumulated force to obtain the force of each basic element in the Hierarchy structure within the preset range of the distance of the current target basic element on the current target basic element.

[0019] The intermediate layer of the Hierarchy structure in step S1 is obtained by biological / chemical experience and / or clustering algorithm. For the case of repeated units in the intermediate layer, only the content of one unit in the repeated unit and the position information of the unit in the molecular system are stored. The repeated unit is a short sequence with the longest same information, or a short sequence with the same information of a certain length determined according to actual needs.

[0020] The end condition in step S5 is the end of a process, or the end condition is that the molecular system to be simulated reaches a balanced stable state.

[0021] The information of the basic element in step S1 is atomic level information or molecular level information.

[0022] The index in step S2 is used to find the position of the corresponding basic element of each unit or space unit, and the loading task is distributed to different threads to quickly query the position and force information of the queried basic element.

[0023] The second aspect of the present application provides a computer readable storage and processing device, which stores computer executable instructions for executing the above-mentioned molecular system processing method related to molecular dynamics simulation.

[0024] The third aspect of the present application provides a molecular system processing device related to molecular dynamics simulation, comprising a construction module, a reconstruction module, a processing module, an acquisition module and a judgment module.

[0025] The constructing module is configured to construct a molecular system to be simulated by using a Hierarchy structure; wherein, a top layer of the Hierarchy structure, i.e., the uppermost layer, comprises all information of the molecular system to be simulated composed of one or more than one unit; a bottom layer of the Hierarchy structure comprises information of basic elements determined according to simulation accuracy, such as atomic level information or molecular level information; between the top layer and the bottom layer of the Hierarchy structure, one or more than one intermediate layer is included according to decomposition of a chemical structure of the molecular system to be simulated, and each intermediate layer comprises one or more than one unit;

[0026] The reconstructing module is configured to reconstruct the Hierarchy structure to obtain a balanced tree Hierarchy structure, and the balanced tree Hierarchy structure comprises the top layer of the Hierarchy structure and one or more than one spatial unit; wherein, each spatial unit comprises one or more than one basic element, and distances between the basic elements are within a preset range; an index is established between each unit or spatial unit and a storage location of the corresponding basic element;

[0027] The processing module is configured to calculate, in a unit of spatial unit, an acting force of each basic element in the balanced tree Hierarchy structure on a current target basic element, and accumulate the acting force

[0028] The obtaining module is configured to obtain state information of the current target basic element according to the accumulated acting force, and return to the processing module until all basic elements of the balanced tree Hierarchy structure are traversed.

[0029] The judging module is configured to end when a preset ending condition is met, and return to the processing module when the ending condition is not met.

[0030] The molecular dynamics simulation method of the present application constructs a molecular system to be simulated by using a Hierarchy structure, and reconstructs the Hierarchy structure to obtain a balanced tree Hierarchy structure; data of each basic element in a spatial unit included in the balanced tree Hierarchy structure is updated by itself, and data iteration is performed to other spatial units until complete update of the top layer of the balanced tree Hierarchy structure is achieved; moreover, during simulation, the Hierarchy structure is connected with an actual molecular data file by using an index, so that contents of a unit or a spatial unit to be loaded are quickly found, thereby providing a fast positioning capability and improving operation efficiency.

[0031] Further, the present application can obtain repeated units with same information in the molecular system to be simulated by the clustering algorithm, and for the repeated units, only the detailed content of one unit and the position information of the unit are stored in the Hierarchy structure of the present application, thereby reducing the memory consumption.

[0032] The present application has the advantage of improving the operation efficiency of the molecular dynamics simulation. BRIEF DESCRIPTION OF DRAWINGS

[0033] The accompanying drawings are included to provide a further understanding of the technical scheme of the present application, and constitute a part of the specification, and are used together with the embodiments of the present application to explain the technical scheme of the present application, and do not constitute a limitation on the technical scheme of the present application.

[0034] Figure 1 The flowchart of the method for processing the molecular system of the molecular dynamics simulation in the embodiments of the present application is shown;

[0035] Figure 2 The embodiment diagram of obtaining the repeated units by the clustering algorithm in the embodiments of the present application is shown;

[0036] Figure 3 The decomposition example diagram of taking one amino acid chain as the molecular system to be simulated in the embodiments of the present application is shown;

[0037] Fig. 4(a) is an example diagram of all basic elements under the Hierarchy structure in the embodiments of the present application;

[0038] Fig. 4(b) is an example diagram of some basic elements belonging to multiple space units in the embodiments of the present application;

[0039] Fig. 4(c) is an example diagram of recursively inserting the basic elements under the Hierarchy structure with distance in the preset range into the four space units corresponding to the four child nodes of the quadtree in the embodiments of the present application;

[0040] Figure 5 The composition structure diagram of the molecular dynamics simulation device in the embodiments of the present application is shown. DETAILED DESCRIPTION

[0041] In order to make the purpose, technical scheme and advantages of the present application more clear and obvious, the embodiments of the present application will be described in detail below with reference to the drawings. It should be noted that the embodiments in the present application and the features in the embodiments can be combined with each other arbitrarily without conflict.

[0042] For the purpose of understanding the present application, the present application will be described in greater detail below with reference to the accompanying drawings. The embodiments of the present application are illustrated in the drawings. However, the present application can be embodied in many different forms and should not be construed as limited to the embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete, and fully convey the scope of the application to those skilled in the art.

[0043] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this application belongs. The terminology used in the description of the application herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the application.

[0044] It should be understood that the terms "first", "second" and the like in the context of the description are used for descriptive purposes only and not intended to connote or imply that a quantity of the identified elements must be present. Thus, a feature described as "first" can implicitly or explicitly include one or more of the same feature.

[0045] It should be understood that, in the following embodiments, "connection" between circuits, modules, units, etc. connected to each other should be understood as "electrical connection", "communication connection", etc. if there is transmission of electrical signals or data between them.

[0046] As used herein, the singular forms "a", "an" and "the" include plural referents unless the context clearly dictates otherwise. It should be understood that the term "comprises / comprising" or "has / have" specifies the presence of stated features, integers, steps, operations, components, parts, or combinations thereof, but does not preclude the presence or addition of one or more other features, integers, steps, operations, components, parts, or combinations thereof.

[0047] The steps shown in the flowchart of the accompanying drawings can be executed in a computer system such as a set of computer-executable instructions. Also, although a logical order is shown in the flowchart, in some cases, the steps shown or described can be executed in an order different from that shown here.

[0048] Molecular dynamics is a cutting-edge technology that combines mathematics, physics, chemistry, and biology. Molecular dynamics is a computational science task that simulates the motion of atoms and molecules to reveal the dynamic behavior of molecular systems, including vibration, conformational change, and interaction, providing key understanding and prediction capabilities for research fields including biology, materials science, and chemistry. This simulation of the motion state of molecules and atoms in a system over a certain period of time allows for dynamic observation of the evolution of the system over time, which can be used to reveal the microscopic physical processes of chemical reactions, for photosynthesis, new drug discovery, and prediction of nanomaterial properties.

[0049] Embodiment 1 Figure 1 As shown in the flowchart of the molecular dynamics simulation method in the embodiments of the present application, the embodiments provide a molecular system processing method for molecular dynamics simulation, including the following steps: Figure 1

[0050] Step 100: Constructing a molecular system to be simulated using a Hierarchy structure.

[0051] The top layer of the Hierarchy structure, i.e., the top level, includes all information of the molecular system to be simulated composed of one or more cells;

[0052] The bottom layer of the Hierarchy structure includes information of basic elements determined according to simulation accuracy, such as atomic-level information or molecular-level information;

[0053] Between the top layer and the bottom layer of the Hierarchy structure, there are one or more intermediate layers decomposed according to the chemical structure of the molecular system to be simulated, and each intermediate layer includes one or more cells.

[0054] In an exemplary example, the Hierarchy structure can be a tree structure used to describe the hierarchical relationship between elements. In the tree structure, there is a root node (e.g., the top layer in the embodiments of the present application), then branches out multiple child nodes (e.g., the intermediate layers in the embodiments of the present application), each child node can have its own child nodes (e.g., the intermediate layers in the embodiments of the present application), and so on, until the last child node (e.g., the bottom layer in the embodiments of the present application), forming a hierarchical relationship.

[0055] ​In an example, the scale requirement to be simulated determines that the information of the basic elements included in the lowest level of the Hierarchy structure is atomic level information or molecular level information. For example, the scale requirement is high, i.e., the simulation precision is high, and the lowest level of the Hierarchy structure can be atomic level information. For another example, the scale requirement is not high, i.e., the simulation precision is not high, and the lowest level of the Hierarchy structure can be small molecule level information or large molecule level information.

[0056] In an example, the middle level of the Hierarchy structure can be obtained by biological / chemical experience and / or a clustering algorithm.

[0057] In an example, examples obtained by biological (or chemical) experience can include, but are not limited to, for example: basic chemical groups composed of atoms and small molecules (such as hydroxyl carboxyl, water molecules, etc.) can be the upper level of atoms; for another example: larger molecular structures composed of basic chemical groups (such as amino acids in protein molecules) can be the upper level of basic chemical groups; for another example: a plurality of amino acid chains form a protein, and the protein is the upper level of the plurality of amino acid chains.

[0058] In an example, examples obtained by a clustering algorithm can include, but are not limited to, for example: there are many repeating units in an amino acid chain (the amino acid chain can be considered to be composed of many different amino acids, and there are many repeating short sequences of amino acids), and the repeating short sequences of amino acids can be clustered as repeating units to be the next level of the amino acid chain, so as to reduce the memory consumption. Figure 2 Taking the amino acid chain ABCDABCA shown in the figure as an example, the amino acid chain ABCDABCA includes different amino acids such as ABC, D, and A, wherein ABC is a repeating short sequence of amino acids. Therefore, the information of the molecule at the next level of the amino acid chain ABCDABCA can include the short sequence of amino acids ABC (indicating two different positions), and the amino acid D and the amino acid A. That is, in the Hierarchy structure in the example, for repeating units, i.e., many units are the same, only the detailed content of one unit and the position information of the unit in the molecular system can be stored, thereby reducing the memory consumption.

[0059] In an example, the repeating unit can be a short sequence with the longest same information, or a short sequence with the same information of a certain length determined according to actual requirements. For example, in the amino acid chain ABCDABCA, in an example, the longest short sequence with the same information, i.e., the short sequence of amino acids ABC, can be a repeating unit. In another example, a short sequence with the same information of a certain length, i.e., the short sequence of amino acids AB, can be a repeating unit according to actual requirements.

[0060] Taking an amino acid chain AGVAGA as a molecular system to be simulated as an example, in this embodiment, a high scale requirement, i.e., a high simulation precision, is taken as an example, wherein A, G and V in the amino acid chain AGVAGA represent glycine, alanine and valine respectively, as shown in the following formula: Figure 3 As shown in the following formula, the Top Level of the Hierarchy structure covers the information of all molecules included in the molecular system to be simulated, including a first cell 1, a second cell 2, a third cell 3, a fourth cell 4, a fifth cell 5 and a sixth cell 6, Figure 3 which are represented by numbers 1-6 respectively in the following formula. As shown in the following formula, Figure 3 the first cell and the sixth cell are other components of the amino acid chain AGVAGA, such as the H atom of the first cell and the OH group of the sixth cell in this embodiment; the second cell and the fourth cell are each composed of a seventh cell 7 and an eighth cell 8, Figure 3 which are represented by numbers 7 and 8 respectively in the following formula, the seventh cell is glycine A, and the eighth cell is alanine G, and the second cell and the fourth cell are each an amino acid short sequence composed of glycine A and alanine G. The third cell is valine V. The fifth cell is glycine A.

[0061] Figure 3 As shown in the following formula, taking the decomposition of glycine A in the second cell or the fourth cell in the Hierarchy structure as an example, the next layer of the intermediate layer of the Top Level of the Hierarchy structure includes the seventh cell 7 and the eighth cell 8, and identifies that the amino acid short sequence composed of glycine A and alanine G appears at two positions of the amino acid chain AGVAGA. As shown in the following formula, Figure 3 According to biological (chemical) experience and / or clustering algorithm, glycine A continues to be decomposed, as shown in the following formula, the next layer of the intermediate layer of glycine A can include some units of basic chemical groups and small molecules composed of atoms, such as one of the units being a group NH For example, one of the units is a group CH For example, one of the units is a group CH3 For example, one of the units is a group CO These units of basic chemical groups and small molecules composed of atoms continue to be decomposed, and the bottom layer of the branch decomposition of glycine A can be obtained, as shown in the following formula, including an atom N, an atom C, an atom H and an atom O, wherein the atom C and the atom H are repeated units, and will identify their positions in different units of the previous layer. Figure 3 Figure 3 ​The amino acid decomposition process of other units is similar to the decomposition process of glycine A, and those skilled in the art can easily implement the decomposition process of glycine A in the embodiments of the present application, which will not be repeated here.

[0062] Step 101: reconstructing the Hierarchy structure to obtain a balanced tree Hierarchy structure, the balanced tree Hierarchy structure including a top layer of the Hierarchy structure and one or more spatial units; wherein each spatial unit includes one or more basic elements, and the distance between the basic elements is within a preset range.

[0063] In an exemplary example, the Hierarchy structure can be reconstructed using one of the following: quadtree (Quad-tree), region tree (R-tree), etc.

[0064] In an exemplary example, reconstructing the Hierarchy structure can include:

[0065] extracting all basic elements from the constructed Hierarchy structure;

[0066] According to the distance between the basic elements, the basic elements with a distance within a preset range are divided into one or more spatial units to obtain a balanced tree Hierarchy structure composed of spatial units and root nodes of the Hierarchy structure.

[0067] In the embodiments of the present application, the Hierarchy structure of any hierarchical structure is reconstructed into a balanced tree structure, which is beneficial to realize more efficient query and operation.

[0068] In an embodiment, taking a quadtree as an example, the quadtree is a tree data structure used to recursively divide two-dimensional space in order to quickly perform insertion, deletion and query operations. The quadtree recursively bisects the two-dimensional space into four spatial regions. At this time, the reconstruction of the Hierarchy structure in step 101 can include:

[0069] defining a quadtree node class, i.e. creating a class containing four child nodes and node data;

[0070] extracting all basic elements from the constructed Hierarchy structure; as shown in FIG. 4(a), an example of all basic elements under the Hierarchy structure is shown, which includes basic elements 1 (elem1), elem2, … elem10;

[0071] According to all the extracted basic elements, the basic elements with distance in the preset range are recursively inserted into the space units corresponding to the child nodes of the quadtree according to the distance between the basic elements, to obtain the balanced tree Hierarchy structure. As shown in FIG. 4(c), an example of recursively inserting the basic elements with distance in the preset range into four space units corresponding to four child nodes of the quadtree is shown.

[0072] It should be noted that if some basic elements as shown in FIG. 4(b) can belong to multiple space units, the region range can be adjusted so that the basic elements are inserted into one of the space units. It should be noted that the space unit in which the basic elements are inserted is the one that makes the obtained balanced tree Hierarchy structure more balanced.

[0073] In this embodiment, the data in the hierarchical structure is organized according to the quadtree structure, which is beneficial to realize efficient spatial query and management, not only ensuring the balance of the tree, but also improving the query efficiency.

[0074] In an exemplary example, in order to make the obtained balanced tree Hierarchy structure more balanced, all the extracted basic elements can be distributed as evenly as possible in the space units corresponding to each child node of the quadtree or region tree.

[0075] In an exemplary example, in order to make the obtained balanced tree Hierarchy structure more balanced, when inserting the extracted basic elements, the region division of the space unit can be further dynamically adjusted to ensure that the load of each child node is as uniform as possible.

[0076] Step 102: Calculate the force of each basic element in the balanced tree Hierarchy structure on the current target basic element and accumulate it, respectively, in units of space units, and each basic element in the space unit as the current target basic element.

[0077] In the present embodiment, in molecular dynamics, the interaction between molecules is local (mainly chemical bonds, van der Waals forces), that is, only some molecules that are relatively close to each other will affect each other. In the present embodiment, the distance between the basic elements included in the space unit is within the preset range, so when calculating the force on a molecule, the present embodiment only needs to consider the influence of the molecules within a certain range near the molecule, and does not calculate the influence of the molecules not within the certain range near the molecule. This greatly improves the operation efficiency.

[0078] In the embodiments of the present application, in the molecular dynamics, when the intermolecular force is calculated, the space unit where the target element is located needs to reach an equilibrium state. In the equilibrium state, the macroscopic properties of the space unit such as energy and density do not change with time, and the distribution and movement of the molecules also have certain regularity. At this time, the intermolecular force is calculated, and the average force of the molecules can be obtained, so that the interaction rule between the molecules can be better understood.

[0079] In an exemplary example, the calculation of the force of each basic element other than the current target basic element in the balance tree Hierarchy structure and the accumulation in step 101 can include:

[0080] In the space unit where the current target basic element is located, the force of each basic element other than the current target basic element is calculated respectively, and the obtained forces are accumulated to obtain a first accumulated force;

[0081] In other space units of the space unit where the current target basic element is located, the force of each basic element in the other space units on the current target basic element is calculated respectively, and the obtained forces are accumulated to obtain a second accumulated force;

[0082] The first accumulated force and the second accumulated force are accumulated to obtain the force of each basic element other than the current target basic element in the balance tree Hierarchy structure on the current target basic element whose distance is within a preset range.

[0083] Step 103: Obtain the state information of the current target basic element according to the accumulated force, and return to step 102 until all the basic elements of the balance tree Hierarchy structure are traversed.

[0084] In an exemplary example, the state information can include but is not limited to, for example, position, velocity, acceleration, etc. It should be noted that the specific implementation of calculating the state information of the current target basic element according to the obtained force does not limit the protection scope of the present application, and will not be described here.

[0085] Step 104: Determine whether a preset end condition is met. If the end condition is met, the process ends; if the end condition is not met, return to step 102.

[0086] In an exemplary example, the end condition can be that the molecular system to be simulated reaches an equilibrium state, and the calculation of the intermolecular force of all or target elements is completed, or a long period of time, i.e., a preset time length, is elapsed.

[0087] In an embodiment, the equilibrium state refers to a state in which the position of each molecule in the entire molecular system presents a periodic (e.g., every time length t) slight change, such as: at time t0, the state information of all molecules in the molecular system is recorded, at time (t0+t), the state information is recorded again, and at time (t0+2*t), the state information is recorded again. In this way, the state information of all molecules in the molecular system is recorded every time length t. When the state information of each molecule in the molecular system recorded each time is substantially the same (i.e., changes very little, such as within a certain range), it can be considered that the molecular system has reached an equilibrium state.

[0088] In an embodiment, after a long period of time, such as a preset time length, the simulation of molecular dynamics can fail, that is, the molecular system to be simulated has not found an equilibrium state. At this time, the process is not simulated until the end, but is ended. That is, a longest simulation end time limit is set, and the timeout means that the simulation is terminated.

[0089] In an embodiment, before the end condition is met, if the position of a molecule (or atom) in the equilibrium tree Hierarchy structure changes, the equilibrium tree Hierarchy structure is updated by the molecular dynamics simulation method provided in the embodiment, so that the update of the state information changes in real time with the slight change of the equilibrium tree Hierarchy structure at this time.

[0090] In an embodiment, because the equilibrium tree Hierarchy structure is constructed on the basis of atoms, and the process of molecular dynamics simulation generally does not include complex physical reactions and chemical reactions, that is, the atoms herein will not increase or decrease, and most chemical bonds will not break, so the update of the equilibrium tree Hierarchy structure is very rare and does not need to be reconstructed. However, it should be noted that when the same cell of the equilibrium tree Hierarchy structure appears in different positions, the state information of the cells in different positions is different. For example, as shown in the equilibrium tree Hierarchy structure, the actual content of the second unit 2 and the fourth unit 4 included in the top level is the same, which is the amino acid short sequence AG, but the two amino acid short sequences AG are in different environments, and thus the state information is different. The state information of the same cell in different positions needs to be updated. Figure 3 As shown in the equilibrium tree Hierarchy structure, the actual content of the second unit 2 and the fourth unit 4 included in the top level is the same, which is the amino acid short sequence AG, but the two amino acid short sequences AG are in different environments, and thus the state information is different. The state information of the same cell in different positions needs to be updated.

[0091] As shown in the equilibrium tree Hierarchy structure, the actual content of the second unit 2 and the fourth unit 4 included in the top level is the same, which is the amino acid short sequence AG, but the two amino acid short sequences AG are in different environments, and thus the state information is different. The state information of the same cell in different positions needs to be updated.

[0092] In this embodiment, taking the first basic element elem1 shown in bold in the upper left space unit in FIG. 4(c) as an example, first, the force of each basic element on the current target basic element is calculated in the space unit where the first basic element elem1 is located, and the obtained forces are added to obtain the first accumulated force, that is, the force of the sixth basic element elem6 on the first basic element elem1 is calculated to obtain the first accumulated force; then, the force of each basic element in other space units on the first basic element elem1 is calculated in other space units of the space unit where the first basic element elem1 is located, and the obtained forces are added to obtain the second accumulated force, taking the upper right space unit in FIG. 4(c) as an example, that is, the force of the seventh basic element elem7 on the first basic element elem1, the force of the eighth basic element elem8 on the first basic element elem1, the force of the ninth basic element elem9 on the first basic element elem1, and the force of the tenth basic element elem10 on the first basic element elem1 are calculated to obtain the force of each basic element in the upper right space unit on the first basic element elem1, and the force of each basic element in the lower left space unit on the first basic element elem1 and the force of each basic element in the lower right space unit on the first basic element elem1 are calculated, and then the forces are added to obtain the second accumulated force. In this way, the first accumulated force and the second accumulated force are added to obtain the force of each basic element in the balance tree Hierarchy structure within the preset range on the first basic element elem1.

[0093] The balance tree Hierarchy structure in the embodiment of the present application is used to accelerate the process of algorithm iteration, each basic element itself updates data and iterates data to other space units until the complete update of the Top Level, solving the problems of too large data volume and too concentrated operation, and further promoting the feasibility of distributed design.

[0094] In an example, in the molecular dynamics simulation process provided by the embodiments of the present application, each cell or space unit is separated from its content (basic elements such as molecular data). In the embodiments of the present application, the mapping relationship between each cell or space unit and the storage location (hard disk address) of its corresponding basic element is established through an index. Through the index, the corresponding content of a certain cell or space unit can be directly found without traversing all data files. In this way, through the index, the Hierarchy hierarchical structure is connected with the actual molecular data file, the content of the cell or space unit to be loaded is quickly found, and the ability of fast positioning is provided.

[0095] In an embodiment, the intermediate result is very large data, which is generally stored as a file on a hard disk. After the simulation is completed, all the files are loaded and a video is generated frame by frame. In fast loading, the index tells the system which files should be loaded by each thread. The system finds the data location of each cell or space unit through the index table and assigns the loading task to different threads.

[0096] In an embodiment, when a specific detail in a local range needs to be focused on, the local range does not need to be cropped after being loaded in its entirety, but can be directly loaded locally. In local loading, the index provides the ability to load only some cells or space units. If only a local range (such as cell_A and cell_C) needs to be viewed, the corresponding files are found through the index, and the system directly loads these files while skipping other cells or space units.

[0097] Embodiment 2

[0098] The embodiment provides a computer readable storage medium, which stores computer executable instructions. The computer executable instructions are used to implement the molecular system processing method for molecular dynamics simulation according to the embodiment 1.

[0099] Embodiment 3

[0100] The embodiment provides a computer device, which comprises a memory and a processor. The memory stores instructions executable by the processor, which are used to implement the molecular system processing method for molecular dynamics simulation according to the embodiment 1.

[0101] Embodiment 4

[0102] The embodiment provides a molecular system processing device for molecular dynamics simulation, as shown in the accompanying drawings, which comprises a construction module, a reconstruction module, a processing module and a judgment module. Figure 5

[0103] ​The constructing module is configured to construct a molecular system to be simulated by using a Hierarchy structure; wherein, a top layer of the Hierarchy structure, i.e. the uppermost layer, comprises all information of the molecular system to be simulated composed of one or more than one unit; a bottom layer of the Hierarchy structure comprises information of basic elements determined according to simulation accuracy, such as atomic level information or molecular level information; between the top layer and the bottom layer of the Hierarchy structure, one or more than one intermediate layer is included according to decomposition of the chemical structure of the molecular system to be simulated, and each intermediate layer comprises one or more than one unit;

[0104] The reconstructing module is configured to reconstruct the Hierarchy structure to obtain a balanced tree Hierarchy structure, and the balanced tree Hierarchy structure comprises the top layer of the Hierarchy structure and one or more than one spatial unit; wherein, each spatial unit comprises one or more than one basic element, and distances between the basic elements are within a preset range;

[0105] The processing module is configured to calculate, as a unit of the spatial unit, an acting force of each basic element in the balanced tree Hierarchy structure on a current target basic element and accumulate the acting force;

[0106] The obtaining module is configured to obtain state information of the current target basic element according to the accumulated acting force, and return to the processing module until all the basic elements of the balanced tree Hierarchy structure are traversed;

[0107] The judging module is configured to end the flow when a preset ending condition is met, and return to the processing module for continuous processing when the ending condition is not met.

[0108] In an exemplary instance, the reconstructing module can be configured to:

[0109] extract all the basic elements from the constructed Hierarchy structure;

[0110] divide the basic elements with distances within a preset range into one or more than one spatial unit according to distances between the basic elements, so as to obtain the balanced tree Hierarchy structure composed of the spatial unit and the root node of the Hierarchy structure.

[0111] In an embodiment, for the case of reconstructing the Hierarchy structure by using a quad-tree, the reconstructing module can be configured to:

[0112] define a quad-tree node class, and create a class containing four child nodes and node data;

[0113] extracting all basic elements from the constructed Hierarchy structure;

[0114] According to the extracted all basic elements, the basic elements with distance in the preset range are recursively inserted into the space unit corresponding to the child node of the quadtree according to the distance between the basic elements, to obtain the balanced tree Hierarchy structure.

[0115] In an exemplary instance, in the processing module, taking each basic element in the space unit as a current target basic element, respectively calculating the force of each basic element in the balanced tree Hierarchy structure on the current target basic element and accumulating, can include: calculating the force of each basic element on the current target basic element in the space unit where the current target basic element is located, and accumulating the obtained force to obtain a first accumulated force;

[0116] calculating the force of each basic element in the other space unit on the current target basic element, and accumulating the obtained force to obtain a second accumulated force;

[0117] accumulating the first accumulated force and the second accumulated force to obtain the force of each basic element in the balanced tree Hierarchy structure with distance in the preset range from the current target basic element on the current target basic element.

[0118] The molecular system processing device provided by the embodiment of the present application is related to molecular dynamics simulation, and the molecular system to be simulated is constructed by using the balanced tree Hierarchy structure obtained by reconstructing the Hierarchy structure, which greatly reduces the judgment of the force between many atoms that do not affect each other, and greatly improves the operation efficiency.

[0119] In an exemplary instance, the intermediate level of the Hierarchy structure in the construction module can be obtained by biological (chemical) experience and / or clustering algorithm, etc. In an embodiment, the repeating unit with the same information in the molecular system to be simulated can be obtained by the clustering algorithm. For the repeating unit, only the detailed content of one unit and the multiple position information of the unit are stored in the Hierarchy structure in the embodiment of the present application. In an embodiment, the repeating unit can be the longest short sequence with the same information, or a short sequence with the same information with a certain length determined according to actual needs. In the Hierarchy structure in the embodiment of the present application, for the repeating unit, only the detailed content of one unit and the multiple position information of the unit are stored, which reduces the memory consumption.

[0120] Although the present application has been described with reference to the above embodiments, the contents described are merely employed embodiments for facilitating the understanding of the present application, and are not intended to limit the present application. Any modification and change in the form and details can be made by any person skilled in the art without departing from the spirit and scope of the present application, and the patent protection scope of the present application shall be subject to the scope defined by the appended claims.

Claims

1. A method for processing molecular systems for molecular dynamics simulation, characterized in that: include: S1. Constructing a molecular system to be simulated using a hierarchical hierarchy; wherein the top layer of the hierarchy includes all information about the molecular system to be simulated, which is composed of one or more units; the bottom layer of the hierarchy includes information about basic elements determined based on simulation accuracy; between the top and bottom layers of the hierarchy, there are one or more intermediate layers decomposed according to the chemical structure of the molecular system to be simulated, each intermediate layer including one or more units; S2. Reconstructing the hierarchy structure to obtain a balanced tree hierarchy structure, wherein the balanced tree hierarchy structure includes a top level of the hierarchy structure and one or more spatial units; wherein each spatial unit includes one or more basic elements, and each spatial unit is loaded as evenly as possible, and the distance between basic elements is within a preset range; and establishing an index between each unit or spatial unit and the storage location of its corresponding basic element; S3. Taking a spatial unit as a unit, each basic element in the spatial unit is used as the current target basic element. After the region where the target element is located reaches a balanced state, the forces exerted by each other basic element in the balanced tree hierarchy on the current target basic element are calculated and accumulated. At the same time, the movement process of the basic element from the unbalanced state to the balanced state within a time period is recorded and saved; S4. Obtain the state information of the current target basic element according to the accumulated force, calculate the force of each other basic element in the balanced tree hierarchy structure on the current target basic element and accumulate the force until all basic elements of the balanced tree hierarchy structure are traversed; S5. Determine whether a preset end condition is met. If so, end; if not, return to the step of calculating and accumulating the forces exerted by each of the other basic elements in the balanced tree hierarchy on the current target basic element.

2. The molecular system processing method for molecular dynamics simulation according to claim 1, characterized in that: The reconstruction of the Hierarchy structure in step S2 includes: S21. Reconstructing the Hierarchy structure using a quadtree or an R-tree, including: defining a node class of the quadtree or the R-tree, and creating a class containing child nodes and node data; S22. Extract all basic elements from the constructed hierarchy structure, and recursively insert the basic elements within a preset distance range into the spatial units corresponding to the child nodes of the quadtree according to the distance between the basic elements, so as to obtain the balanced tree hierarchy structure; S23. According to the molecular dynamics simulation method according to claim S22, the area division of the spatial unit is dynamically adjusted to make the load of each sub-node uniform.

3. The molecular system processing method for molecular dynamics simulation according to claim 1, characterized in that: The calculation of the force exerted by each other basic element in the balanced tree hierarchy structure on the current target basic element and the accumulation of the force in step S3 include: S31. Within the spatial unit where the current target basic element is located, when the target element reaches a state of equilibrium, record the state information of the target element at this time, calculate the force exerted by each other basic element on the current target basic element, and accumulate the obtained forces to obtain a first accumulated force; S32. Calculate the force exerted by each basic element in the other spatial units on the current target basic element in the spatial unit where the current target basic element is located, and accumulate the obtained forces to obtain a second accumulated force; S33. Accumulate the first accumulated force and the second accumulated force to obtain the force exerted by each other basic element in the balanced tree hierarchy structure whose distance from the current target basic element is within a preset range on the current target basic element.

4. The molecular system processing method for molecular dynamics simulation according to claim 1, characterized in that: The middle layer of the Hierarchy structure described in step S1 is obtained through biological / chemical experience and / or clustering algorithm. For the case of repeating units in the middle layer, only the content of one unit in the repeating unit and the position information of the unit in the molecular system are stored. The repeating unit is the longest short sequence with the same information, or a short sequence with the same information of a certain length determined according to actual needs.

5. The molecular system processing method for molecular dynamics simulation according to claim 1, characterized in that: The end condition in step S5 is the end of a process, or the molecular system to be simulated reaches a stable equilibrium state.

6. The molecular system processing method for molecular dynamics simulation according to claim 1, characterized in that: The information of the basic elements in step S1 is information at the atomic level or information at the molecular level.

7. The method for processing a molecular system for molecular dynamics simulation according to any one of claims 1 to 6, characterized in that: The position of the basic element corresponding to each unit or spatial unit is searched through the index described in step S2, and the loading task is assigned to different threads, so as to query the position and force information of the queried basic element in a fast loading manner.

8. A computer device comprising a memory and a processor, wherein: The memory stores the following instructions that can be executed by the processor: instructions for executing the steps of the molecular system processing method for molecular dynamics simulation according to any one of claims 1 to 7.

9. A molecular system processing device for molecular dynamics simulation, characterized in that: include: Construction module, reconstruction module, processing module, acquisition module, judgment module; among them, S91. A construction module for constructing a molecular system to be simulated using a hierarchy structure; wherein the top layer of the hierarchy structure, i.e., the uppermost layer, includes all information of the molecular system to be simulated, which is composed of one or more units; the bottom layer of the hierarchy structure includes information of basic elements determined according to simulation accuracy, such as atomic-level information or molecular-level information; between the top and bottom layers of the hierarchy structure, one or more intermediate layers are included, each intermediate layer including one or more units; S92. A reconstruction module is configured to reconstruct the hierarchy structure to obtain a balanced tree hierarchy structure, wherein the balanced tree hierarchy structure includes a top layer of the hierarchy structure and one or more spatial units; wherein each spatial unit includes one or more basic elements, and the distance between the basic elements is within a preset range; and an index is established between each unit or spatial unit and the storage location of its corresponding basic element; S93. A processing module for calculating the force of each basic element in the balanced tree hierarchy structure on the current target basic element and accumulating the force, and recording the state information of the target element at this time, with each basic element in the spatial unit as the current target basic element. S94. An acquisition module is configured to obtain status information of the current target basic element according to the accumulated force, and return to the processing module until all basic elements of the balanced tree hierarchy structure are traversed; S95 is a judgment module, which is used to end the process when a preset end condition is met, and return to the processing module when the end condition is not met.

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