Polymer molecular dynamics calculation method and polymer molecular dynamics calculation device

Abstract

To provide a method and device for calculating molecular dynamics of a polymer, which facilitate the access to molecular information constituting the polymer included in a calculation system.SOLUTION: A calculation method in a device for calculating molecular dynamics of a polymer, includes: a model creation step of creating a model of a molecular structure of a polymer which performs molecular dynamics calculation; and a calculation step of performing the molecular dynamics calculation using a system including the model. In the model creation step, a method for calculating the molecular dynamics of the polymer is provided, which gives an identification symbol for identification for each unit structure of a repeated structure of a polymer. The identification symbol includes: a label corresponding to a type of the unit structure; and a number assigned for each unit structure in the repeated structure.SELECTED DRAWING: Figure 2

Description

[Technical Field]

[0001] The present invention relates to a polymer molecular dynamics calculation method and a polymer molecular dynamics calculation device. [Background technology]

[0002] As disclosed in Patent Document 1 and the like, molecular dynamics has traditionally been used as a method for analyzing the motion and energy of atoms and molecules, and in recent years, with improvements in computer performance, it has also come to be applied to polymers and the like containing a large number of atoms. [Prior art documents] [Patent documents]

[0003] [Patent Document 1] Japanese Patent Application Laid-Open No. 2011-248541 Summary of the Invention [Problem to be solved by the invention]

[0004] When performing molecular dynamics calculations, in most cases, a whole system is created by combining molecular models created in advance, and then used for the calculation.

[0005] A polymer may be composed of, for example, more than a thousand atoms, but the atoms are only labeled with a letter such as "C" according to their type, and the molecules that are the repeating unit structures of the polymer are not identified. This poses the problem that when performing molecular dynamics calculations on a system that includes a polymer and analyzing molecules at specific positions that make up the polymer or the atoms that those molecules contain, it takes time to access information about the molecules that make up the polymer.

[0006] In view of the problems inherent in the above-described conventional techniques, one aspect of the present invention aims to provide a molecular dynamics calculation method for polymers that facilitates access to molecular information that constitutes the polymers included in the system in which the calculation is performed. [Means for solving the problem]

[0007] In order to solve the above problem, according to one aspect of the present invention, a model creation step in which a computer creates a model of the molecular structure of a polymer included in a system for performing molecular dynamics calculations; a calculation step of performing a molecular dynamics calculation using a system including the model; In the model creation step, an identification symbol is assigned to each unit structure of the repeating structure of the polymer. death, The identification symbol includes a label according to the type of the unit structure and a number assigned to each unit structure within the repeating structure. A method for molecular dynamics calculation of polymers is provided. [Effects of the Invention]

[0008] According to one aspect of the present invention, it is possible to provide a molecular dynamics calculation method for a polymer that facilitates access to molecular information that constitutes a polymer included in a system in which calculations are performed. [Brief explanation of the drawings]

[0009] [Figure 1] FIG. 2 is an explanatory diagram of an example of a unit structure. [Figure 2] FIG. 1 is an explanatory diagram of a unit structure and a repeating structure of a polymer. [Figure 3] 1 is a hardware configuration diagram of a polymer molecular dynamics calculation apparatus according to an embodiment of the present invention. [Figure 4] 1 is a block diagram showing the functions of a polymer molecular dynamics calculation apparatus according to an embodiment of the present invention. FIG. DETAILED DESCRIPTION OF THE INVENTION

[0010] Hereinafter, embodiments for carrying out the present invention will be described, but the present invention is not limited to the following embodiments, and various modifications and substitutions can be made to the following embodiments without departing from the scope of the present invention. [Polymer molecular dynamics calculation method] The polymer molecular dynamics calculation method of this embodiment can include the following model creation step and calculation step.

[0011] In the model creation step, a model of the molecular structure of the polymer contained in the system in which the molecular dynamics calculation is performed can be created.

[0012] In the calculation step, a molecular dynamics calculation can be performed using a system including the model created in the model creation step.

[0013] Each step will be explained below. (Model creation process) In the model creation step, as described above, a model of the molecular structure of the polymer contained in the system in which the molecular dynamics calculation is performed can be created.

[0014] In the model creation process, an identification symbol can be assigned to identify each unit structure of the repeating structure of the polymer.

[0015] The inventors of the present invention have investigated a molecular dynamics calculation method for polymers that facilitates access to molecular information constituting the polymer contained in the calculation system. As a result, they have discovered that it is possible to assign an identification symbol to each unit structure of a repeating structure contained in the polymer. By assigning an identification symbol to each unit structure in this way, it is possible to easily identify and search for a target unit structure when creating a model or analyzing the results of a molecular dynamics calculation. This makes it easy to access molecular information constituting the polymer, i.e., information about a specific unit structure and the atoms contained in the unit structure. Note that molecular information includes various conditions used in molecular dynamics calculations for molecules that are unit structures and atoms that constitute the unit structures, as well as information about the calculation results of the molecular dynamics calculations.

[0016] In molecular dynamics calculation programs, in order to calculate the time evolution of a large number of atoms, it is common to separate the files into a topology file, which is a file containing information such as atomic bonds, and a structure file, which is a file containing the coordinates of each atom. However, when using molecular modeling software, the arrangement of atoms in a molecule may be changed in a manner suitable for the molecular dynamics calculation program being used. As a result, the topology file and the structure file may not correspond to each other. However, according to the molecular dynamics calculation method of this embodiment, by assigning an identification symbol to each unit structure as described above, it is possible to easily detect corresponding unit structures and the atoms that make up the unit structures between the two files, even if the arrangement is changed as described above.

[0017] Here, an example of the procedure for assigning identification symbols in the model creation process will be described.

[0018] Here, an example will be described in which ethyl cellulose is used as the polymer. Ethyl cellulose has a structure represented by the following chemical formula (1), for example.

[0019] The polymer to which the molecular dynamics calculation method for polymers of the present embodiment is applied is not particularly limited, and a polymer containing a repeating structure having a plurality of unit structures can be suitably applied. For example, a polymer containing a repeating structure having 10 or more unit structures is preferred, and a polymer containing a repeating structure having 50 or more unit structures is more preferred.

[0020] [ka] The structure in parentheses in the above chemical formula (1) is a unit structure, and a repeating structure is formed by repeatedly arranging n such unit structures.

[0021] In the model creation process, for example, molecular modeling of the unit structure can be performed first. Specifically, a model of the structure in the parentheses above can be created. For example, as shown in Figure 1, a model of unit structure 10 with the terminal portion capped with a methyl group or the like can be created (unit structure model creation process). In Figure 1, atom 11 is oxygen, atom 12 is carbon, and atom 13 is hydrogen, and the same hatching indicates atoms of the same type.

[0022] When performing molecular modeling of unit structures, it is preferable to assign a label corresponding to the type of unit structure as an identification symbol. For example, the above unit structure can be labeled "EC." By assigning a label corresponding to the type of unit structure in this way, it becomes easier to identify the type of unit structure when performing calculations on a polymer containing multiple types of unit structures.

[0023] Next, a polymer model can be created using the created unit structure (polymer model creation step).

[0024] Specifically, the unit structures are repeatedly arranged, excluding the cap portions of the unit structures created in the unit structure model creation step, to create a model 20 of the molecular structure of a polymer including a repeating structure in which a plurality of unit structures 10 are arranged, as shown in Figure 2. In this case, it is preferable to assign a number to each unit structure in the repeating structure of the polymer as an identification symbol. Specifically, for example, numbers can be assigned to the unit structures from one end side of the repeating structure of the polymer.

[0025] By the above operations, the unit structures constituting the repeating structure of the polymer can be given an identification symbol including "EC," which is a label according to the type of unit structure, and a number assigned to each unit structure within the repeating structure. Specifically, each unit structure 10 constituting the repeating structure of the polymer molecular structure model 20 can be given an identification symbol such as 1EC, 2EC, 3EC, etc. Note that the notation of the identification symbol is not limited to the above configuration and can be expressed arbitrarily.

[0026] In this way, it is preferable that the identifying symbol include a label according to the type of unit structure and a number assigned to each unit structure in the repeating structure, because the identifying symbol includes a label according to the type of unit structure and a number assigned to each unit structure in the repeating structure, which makes it particularly easy to access information about the molecules that make up the polymer from the type of unit structure and the number.

[0027] If necessary, the model creation process may further include a reaction system creation process in which a system for molecular dynamics calculations is created using the created model, and an output process in which a topology file or a structure file is output in a predetermined output format.

[0028] An example of the output structure file is shown in Table 1 below.

[0029] As shown in Table 1, by having an identification symbol that identifies each unit structure within the repeating structure, each unit structure can be easily identified and searched for.

[0030] [Table 1] (calculation process) In the calculation step, a molecular dynamics calculation can be performed using a system including the model created in the model creation step.

[0031] Molecular dynamics calculation is a computer simulation method for the physical movement of atoms, and can determine the time evolution of the atomic positions by numerically solving Newton's equations of motion. Therefore, by performing the calculation step, it is possible to determine the time series changes in the coordinates of each atom included in a system including the model created in the model creation step.

[0032] The molecular dynamics calculation can be performed according to the purpose of the analysis, and the conditions are not particularly limited.

[0033] According to the molecular dynamics calculation method for polymers of this embodiment described above, by assigning an identification symbol to each unit structure of the repeating structure of the polymer, it is possible to easily access molecular information constituting the polymer included in the system in which the calculation is performed. [Polymer molecular dynamics calculation equipment] The polymer molecular dynamics calculation apparatus of this embodiment can have a model creation unit and a calculation unit.

[0034] The model creation unit can create a model of the molecular structure of a polymer included in a system for performing molecular dynamics calculations.

[0035] The calculation unit can perform molecular dynamics calculations using a system including the model created by the model creation unit.

[0036] In the model creation section, an identification symbol can be assigned to identify each unit structure of the repeating structure of the polymer.

[0037] As shown in the hardware configuration diagram of Fig. 3, the polymer molecular dynamics calculation apparatus 30 of this embodiment is configured, for example, by an information processing device (computer), and can be physically configured as a computer system including a CPU (Central Processing Unit: processor) 31, which is an arithmetic processing unit, a RAM (Random Access Memory) 32 and a ROM (Read Only Memory) 33, which are main storage devices, an auxiliary storage device 34, an input / output interface 35, and a display device 36, which is an output device. These are interconnected by a bus 37. The auxiliary storage device 34 and the display device 36 may be provided externally.

[0038] The CPU 31 controls the overall operation of the polymer molecular dynamics calculation apparatus 30 and performs various types of information processing. The CPU 31 executes, for example, a program (polymer molecular dynamics calculation program) described below stored in the ROM 33 or the auxiliary storage device 34, to create a model of the molecular structure of the polymer, perform molecular dynamics calculations, etc.

[0039] The RAM 32 is used as a work area for the CPU 31 and may include a non-volatile RAM for storing main control parameters and information.

[0040] The ROM 33 can store a program (polymer molecular dynamics calculation program) and the like.

[0041] The auxiliary storage device 34 is a storage device such as an SSD (Solid State Drive) or an HDD (Hard Disk Drive), and can store various data, files, etc. required for the operation of the polymer molecular dynamics calculation device.

[0042] The input / output interface 35 includes both a user interface such as a touch panel, keyboard, display screen, and operation buttons, and a communication interface that takes in information from an external data recording server and outputs analysis information to other electronic devices.

[0043] The display device 36 is a monitor display, etc. An analysis screen is displayed on the display device 36, and the screen is updated in response to input / output operations via the input / output interface 35.

[0044] Each function of the polymer molecular dynamics calculation apparatus 30 shown in FIG. 3 can be realized by reading a program (polymer molecular dynamics calculation program) from a main storage device such as RAM 32 or ROM 33 or an auxiliary storage device 34, and executing it with CPU 31, thereby reading and writing data in RAM 32, etc., and operating input / output interface 35 and display device 36.

[0045] FIG. 4 shows a functional block diagram of a polymer molecular dynamics calculation apparatus 30 according to this embodiment.

[0046] 4, polymer molecular dynamics calculation apparatus 30 can have a receiving unit 41, a processing unit 42, and an output unit 43. These units are realized by software and hardware working together in an information processing device such as a personal computer equipped with a CPU, a storage device, various interfaces, etc., of polymer molecular dynamics calculation apparatus 30, by the CPU executing a pre-stored program, such as the above-described polymer molecular dynamics calculation method or polymer molecular dynamics calculation program.

[0047] The configuration of each part will be explained below. (A) Reception The reception unit 41 receives input of commands and data from the user related to the processing executed by the processing device 42. Examples of the reception unit 41 include a keyboard or mouse operated by the user to input commands, a communication device for inputting via a network, and a reading device for inputting from various storage media such as a CD-ROM or DVD-ROM. (B) Processing equipment The processing device 42 may include a model creation unit 421 and a calculation unit 422 . (B-1) Model Creation Section The model creation unit 421 can create a model of the molecular structure of a polymer included in a system for performing molecular dynamics calculations.

[0048] The model creation unit can assign an identification symbol to each unit structure of the repeating structure of the polymer. The identification symbol preferably includes a label corresponding to the type of unit structure and a number assigned to each unit structure within the repeating structure. This is because, by including a label corresponding to the type of unit structure and a number assigned to each unit structure within the repeating structure in the identification symbol, it is possible to particularly easily access information about the molecules that make up the polymer from the type of unit structure and the number. (B-2) Calculation section The calculation unit 422 can perform molecular dynamics calculations using a system including the model created in the model creation step.

[0049] If necessary, the processing device 42 may further include a reaction system creation unit or the like that creates a system for molecular dynamics calculations using the model created by the model creation unit 421. In this case, the calculation unit can perform molecular dynamics calculations using the system created by the reaction system creation unit. (C) Output section The output unit 43 may have a display, etc. It can output the calculation results obtained by the calculation unit 422 and, if necessary, information on the molecular structure model of the polymer created by the model creation unit.

[0050] The content of the calculation results to be output is not particularly limited, but for example, the calculation results can be output and displayed as an image on the output unit 43. In addition, as information on the molecular structure model of the polymer, for example, a topology file or a structure file can be output in a predetermined output format.

[0051] According to the polymer molecular dynamics calculation device of this embodiment described above, by assigning an identification symbol to each unit structure of the repeating structure of the polymer, it is possible to easily access molecular information that constitutes the polymer included in the system in which the calculation is performed. [Polymer molecular dynamics calculation program] Next, the polymer molecular dynamics calculation program of this embodiment will be described.

[0052] The polymer molecular dynamics calculation program of this embodiment can cause a computer to function as the following model creation unit and calculation unit.

[0053] The model creation unit can create a model of the molecular structure of a polymer included in a system for performing molecular dynamics calculations.

[0054] The calculation unit can perform molecular dynamics calculations using a system including the model created in the model creation step.

[0055] In the model creation section, an identification symbol can be assigned to identify each unit structure of the repeating structure of the polymer.

[0056] In addition, the polymer molecular dynamics calculation program of this embodiment can also function as a reaction system creation unit that creates a system for molecular dynamics calculation using the model created by the model creation unit, as needed.

[0057] The polymer molecular dynamics calculation program of this embodiment can be stored in various storage media, such as the RAM or ROM of the polymer molecular dynamics calculation apparatus described above, as a main storage device or auxiliary storage device. By loading the program and executing it with a CPU, data can be read and written from and to the RAM, etc., and the input / output interface and display device can be operated for execution. Therefore, a description of the matters already described for the polymer molecular dynamics calculation apparatus will be omitted.

[0058] The polymer molecular dynamics calculation program of the present embodiment described above may be stored on a computer connected to a network such as the Internet and provided by being downloaded via the network. Also, the polymer molecular dynamics calculation program of the present embodiment may be configured to be provided and distributed via a network such as the Internet.

[0059] The polymer molecular dynamics calculation program of this embodiment may be distributed in a state stored on an optical disk such as a CD-ROM or a recording medium such as a semiconductor memory.

[0060] According to the polymer molecular dynamics calculation program of the present embodiment described above, by assigning an identification symbol to each unit structure of the repeating structure of the polymer, it is possible to easily access molecular information constituting the polymer included in the system in which the calculation is performed. [Explanation of symbols]

[0061] 421 Model Creation Department 422 Calculation Department

Claims

1. a model creation step in which a computer creates a model of the molecular structure of a polymer included in a system for performing molecular dynamics calculations; a calculation step of performing a molecular dynamics calculation using a system including the model; In the model creation step, an identification symbol is assigned to each unit structure of the repeating structure of the polymer, A method for molecular dynamics calculation of polymers, wherein the identification symbol includes a label according to the type of the unit structure and a number assigned to each of the unit structures within the repeating structure.

2. a model creation unit that creates a model of the molecular structure of a polymer included in a system that performs molecular dynamics calculations; a calculation unit that performs molecular dynamics calculations using a system including the model, the model creation unit assigns an identification symbol to each unit structure of a repeating structure of a polymer; The identification symbol includes a label according to the type of the unit structure and a number assigned to each unit structure within the repeating structure.

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