JP-7856219-B2 - Simulation device, simulation method, and program

Inventors

• 遊間 祐一郎
• 平川 皓朗
• 奥野 好成

Assignees

• 株式会社レゾナック

Dates

Publication Date

20260511

Application Date

20240718

Priority Date

20230720

Claims (8)

1. A selection unit configured to select the target coordinates in the structural space, An addition unit configured to add a potential to the aforementioned target coordinates, A calculation unit configured to calculate the time evolution of the structural space in a first time interval by first-principles calculations, A prediction unit is configured to predict the time evolution in a second time interval based on a prediction model in which time is the explanatory variable and the target coordinates changed by the application of an artificial force derived from the potential are the dependent variable, A simulation device equipped with the following features.
2. A simulation apparatus according to claim 1, The system further comprises a learning unit configured to generate the predictive model by learning the calculation results of the aforementioned time evolution. Simulation device.
3. A simulation apparatus according to claim 1 , The system further includes a decision unit configured to determine whether to execute the calculation unit or the prediction unit in the next time interval, based on the difference between the calculated result of the time evolution and the predicted result of the time evolution in the same time interval. Simulation device.
4. A simulation apparatus according to claim 3, The determination unit is configured to be executed after the prediction unit has predicted the time evolution over a predetermined number of time intervals. Simulation device.
5. A simulation apparatus according to any one of claims 1 to 4, The aforementioned potential is a Gaussian function type potential, The aforementioned artificial force is calculated by the following equation, where b is the distance between the target coordinates in the current time interval and the target coordinates in past time intervals, and a and c are fitting functions: Simulation device.
6. A simulation apparatus according to claim 5, The prediction model uses the target coordinates that have been modulated based on the artificial force as the objective variable. The modulation is calculated by the following equation, where F meta is the artificial force, m is the mass of the particles forming the structure corresponding to the target coordinates, and Δt is the length of the time interval: Simulation device.
7. Computers Procedure for selecting target coordinates in structural space, A procedure for adding a potential to the aforementioned target coordinates, A procedure for calculating the time evolution of the structural space in a first time interval by first-principles calculations, A procedure for predicting the time evolution in a second time interval based on a prediction model in which time is the explanatory variable and the target coordinates changed by the application of an artificial force derived from the potential are the dependent variable, A simulation method for performing this.
8. On the computer, Procedure for selecting target coordinates in structural space, A procedure for adding a potential to the aforementioned target coordinates, A procedure for calculating the time evolution of the structural space in a first time interval by first-principles calculations, A procedure for predicting the time evolution in a second time interval based on a prediction model in which time is the explanatory variable and the target coordinates changed by the application of an artificial force derived from the potential are the dependent variable, A program to execute.

Description

This disclosure relates to a simulation apparatus, a simulation method, and a program. Techniques for obtaining free energy surfaces using molecular simulations are known. In this type of technique, reaction pathway exploration methods (metadynamics) are sometimes used to avoid getting stuck in local optima. Metadynamics is a method that enables global sampling by adding a Gaussian potential to sampled reaction coordinates, thereby avoiding re-sampling of already sampled reaction coordinates. For example, Patent Document 1 discloses an invention that uses metadynamics to search for stable binding structures, using the dihedral angle between a target molecule and a candidate drug molecule as a collective variable, in order to efficiently search for multiple stable binding structures. International Publication No. 2019/130529 Figure 1 is a block diagram showing an example of the overall configuration of an information processing system.Figure 2 is a block diagram showing an example of a computer hardware configuration.Figure 3 is a block diagram showing an example of the functional configuration of an information processing system.Figure 4 is a flowchart showing an example of a simulation method. The embodiments of this disclosure will be described below with reference to the accompanying drawings. In this specification and the drawings, components having substantially the same functional configuration are denoted by the same reference numerals, thus omitting redundant descriptions. [Embodiment] One embodiment of the present disclosure is an information processing system for performing molecular simulations. The information processing system in this embodiment has the function of performing molecular simulations to obtain a free energy surface. There are techniques for calculating state variables such as free energy by simulating particles such as atoms or molecules. In this type of technique, the coordinates for calculating the state variables are sometimes sampled from the structural space, and the state variables of those coordinates are repeatedly calculated using first-principles calculations. However, due to limitations such as computational cost relative to time or size, it may not be possible to obtain sufficient samples, potentially leading to the system becoming trapped in local optima. Here, structural space refers to the space that encompasses all the structures that represent the positional and bonding relationships of each particle constituting a substance. The coordinates of structural space correspond to a single structure and indicate the conformation of the particles contained within that structure. An example of structural space is the structural space of a reaction molecular system in which multiple molecules undergo a chemical reaction. One method to prevent getting stuck in local minima is a reaction pathway search technique called metadynamics. In metadynamics, a potential based on a penalty function is added to the sampled coordinates, filling the free energy surface with the potential and avoiding returning to previously sampled coordinates. According to metadynamics, the probability of getting stuck in a local minima is reduced, and global sampling becomes possible. Furthermore, the penalty function is often a Gaussian function. Hereafter, a potential based on a Gaussian function will also be referred to as a "Gaussian potential." In metadynamics, when filling a free energy surface with a potential, the system moves back and forth between similar coordinates before moving out of the free energy surface near the target coordinate. In other words, metadynamics involves repeated sampling within a narrow range during the search for the local optimum. Therefore, obtaining a free energy surface using metadynamics requires significant computational cost for sampling near the local optimum. On the other hand, since the number of possible conformations for a particle is limited near the local optimum, it is expected that the sampling behavior can be predicted quickly and accurately by learning these conformations. One embodiment of this disclosure aims to obtain a free energy surface with low computational cost. In this embodiment, the time evolution of the structural space in a first time interval is calculated by first-principles calculations, and the time evolution of the structural space in a second time interval is predicted based on a predictive model that has learned the calculation results of the time evolution. In one aspect, according to this embodiment, the free energy surface of the reaction molecular system can be obtained in a short time and with high accuracy. <Overall Structure> The overall configuration of the information processing system in this embodiment will be described with reference to Figure 1. Figure 1 is a block diagram showing an example of the overall configuration of the information processing system in this embodiment. As shown in Figure 1, the information proc