Asphaltene molecular dynamics behavior simulation method based on multi-software collaboration

Abstract

The present invention relates to the technical field of molecular dynamics simulation, and in particular to a method for simulating the molecular dynamics behavior of asphaltene based on the collaboration of multiple software, comprising: (1) drawing a molecular model using Materials Studio software; (2) obtaining a force field file of the molecular model through a Python script; (3) constructing a crude oil simulation system using a dynamic modeling method based on topological relationships in Packmol software, and performing energy minimization on the crude oil simulation system in GROMACS software; (4) completing molecular dynamics simulation in GROMACS software; and (5) analyzing the simulation results. The method for simulating the molecular dynamics behavior of asphaltene based on the collaboration of multiple software of the present invention better simulates the dynamic changes between molecules, improves the accuracy and credibility of the simulation, improves the simulation efficiency, and overcomes the functional limitations of using a single software.

Description

Technical Field

[0001] The present invention relates to the technical field of molecular dynamics simulation, and in particular to a method for simulating asphaltene molecular dynamics behavior based on multi-software collaboration. Background Art

[0002] Asphaltenes are the most complex components in crude oil. Their aggregation and deposition are one of the biggest technical challenges facing the oil industry, increasing production costs. Many problems encountered during oil production, processing, and transportation are related to the presence of asphaltene aggregates in the components.

[0003] However, due to the complex composition of asphaltene and the great differences in its internal structure, it is extremely difficult to study its internal structure through experimental means. In addition, the aggregation of asphaltene is closely related to its phase behavior, fluidity, coking and deposition, and is a key factor affecting heavy oil processing. In order to ensure the safe and economical operation of the crude oil production process, it is necessary to reveal the aggregation characteristics of asphaltene at the nanoscale. However, existing asphaltene molecular dynamics simulation methods are often limited to a single molecular dynamics software, resulting in single functionality and low simulation efficiency. In addition, in the field of molecular dynamics simulation, modeling is one of the key steps to achieve high-precision molecular simulation. In the existing technology, static modeling methods are widely used, that is, the structure of the molecule is fixed. In this method, the dynamic behavior within the molecule is often ignored, so the simulation results may be distorted, and the accuracy and credibility of the simulation will be affected. Summary of the Invention

[0004] The technical problem to be solved by the present invention is: in order to solve the problems of single function, low simulation efficiency and low accuracy of simulation results in the existing asphaltene molecular dynamics simulation method, the present invention provides an asphaltene molecular dynamics behavior simulation method based on multi-software collaboration, which better simulates the dynamic changes between molecules, improves the accuracy and credibility of the simulation, improves the simulation efficiency, and solves the limitations of using a single software function.

[0005] The technical solution adopted by the present invention to solve the technical problem is: a method for simulating the molecular dynamics behavior of asphaltene based on multi-software collaboration, which specifically includes the following steps:

[0006] (1) Drawing molecular models:

[0007] constructing four molecular models using the sketch tool of Materials Studio software, and then optimizing the structure of each molecular model using the clean tool of the Materials Studio software;

[0008] Among them, the four molecular models are saturated hydrocarbon molecular model, aromatic hydrocarbon molecular model, colloid molecular model and asphaltene molecular model;

[0009] (2) Molecular force field file:

[0010] Each molecular model file is converted to .mol2 format, a Python script is used to calculate and generate a topology file that can be used by the GROMACS program, and the atomic RESP charges in each molecular model are calculated and verified by the Multiwfn software;

[0011] (III) Construction of crude oil simulation system based on dynamic modeling method of topological relationship:

[0012] In Packmol software, first construct 8×8×8nm 3 A simulation box, dividing the simulation box into multiple sub-areas according to the topological relationship between each of the molecular models;

[0013] sequentially adding the saturated hydrocarbon molecular model, the aromatic hydrocarbon molecular model, the colloid molecular model, and the asphaltene molecular model into the sub-regions, dynamically adjusting the size and shape of each sub-region to accommodate the interaction between each molecular model, and obtaining the crude oil simulation system;

[0014] In GROMACS software, the crude oil simulation system is subjected to an energy minimization program using the steepest descent method to obtain an initial equilibrium system;

[0015] (IV) Molecular dynamics simulation:

[0016] In GROMACS software, the initial equilibrium system is subjected to molecular dynamics simulation at a rate of not less than 30 ns to obtain a trajectory file of molecular motion;

[0017] (V) Analysis of simulation results:

[0018] The evolution of the trajectory file of the molecular motion over time was observed by visual molecular dynamics software, and the dynamic characteristics of the trajectory file of the molecular motion were analyzed by the built-in analysis tool of the GROMACS software.

[0019] Further, specifically, the saturated hydrocarbons include hexane, heptane, octane and wax molecules;

[0020] The aromatic hydrocarbons include benzene and toluene.

[0021] Furthermore, specifically, the Python script may automatically call Antechamber in Ambertools to generate the topology file.

[0022] Further, specifically, the number of the multiple sub-regions is eight sub-regions, and sequentially adding the saturated hydrocarbon molecular model, the aromatic hydrocarbon molecular model, the colloid molecular model, and the asphaltene molecular model to the sub-regions specifically includes the following steps:

[0023] placing the saturated hydrocarbon molecular model into all sub-regions to simulate the situation where the saturated hydrocarbon molecular model exists in the simulation box;

[0024] placing the aromatic hydrocarbon molecule model into the sub-region of the front half along the x, y, and z axes to simulate the situation where the aromatic hydrocarbon molecule mainly exists in the surface layer;

[0025] The colloid molecule model is placed in the sub-region of the latter half along the x, y, and z axes to simulate the situation that the colloid molecule mainly exists in the deep layer;

[0026] The asphaltene molecular model is placed in all sub-regions to simulate the situation where the asphaltene molecular model widely exists in the entire simulation box.

[0027] Furthermore, specifically, the molecular dynamics simulation parameters are NPT ensemble.

[0028] Furthermore, specifically, the temperature control during the molecular dynamics simulation process adopts the V-rescale method.

[0029] Furthermore, specifically, the pressure control during the molecular dynamics simulation process adopts the Berendsen method.

[0030] Furthermore, specifically, during the molecular dynamics simulation, the initial velocity of each molecular model in the crude oil simulation system satisfies the Maxwell-Boltzmann distribution law, the GAFF force field is used to set the crude oil to be infinitely extended in the x, y, and z directions, and periodic boundary conditions are used in each direction; the PME algorithm is used to calculate the long-range Coulomb interaction, and the cutoff radius of the short-range van der Waals interaction and Coulomb interaction is set to All hydrogen bonds were constrained using the LINCS algorithm.

[0031] Furthermore, specifically, the built-in analysis tools of the GROMACS software include radial distribution function, root mean square displacement, self-diffusion coefficient, cluster number and hydrogen bond number.

[0032] The beneficial effects of the present invention are:

[0033] (1) The present invention solves a problem that cannot be solved in experiments and explores the aggregation behavior of asphaltene molecules at the nanoscale;

[0034] (2) The present invention constructs a crude oil simulation system by using a dynamic modeling method based on topological relationships, which can better simulate the dynamic changes between molecules and avoid the limitations of static modeling methods that require fixed molecular structures, thereby improving the accuracy and credibility of the simulation;

[0035] (3) The present invention has a wide range of applications and is applicable to any asphaltene molecular structure model. It can also set crude oil system models with different temperature, pressure conditions, and solvent compositions according to requirements.

[0036] (4) The present invention fully utilizes the advantages of various molecular dynamics software. Materials Studio software can visualize molecular models and optimize molecular configurations. Python scripts can automatically generate molecular topology files. Packmol software can randomly stack specified molecules into specified areas according to custom rules. GROMACS software has fast calculation speed and high parallel efficiency. BRIEF DESCRIPTION OF THE DRAWINGS

[0037] The present invention will be further described below with reference to the accompanying drawings and examples.

[0038] Figure 1 This is a process diagram in the best embodiment of the present invention;

[0039] Figure 2 This is a schematic diagram of model construction in the best embodiment of the present invention;

[0040] Figure 3 Schematic diagram of the simulation box division in the best embodiment of the present invention

[0041] Figure 4 This is a diagram of the asphaltene aggregation model in the best embodiment of the present invention;

[0042] Figure 5 This is the asphaltene radial distribution function diagram in the optimal embodiment of the present invention. DETAILED DESCRIPTION

[0043] The present invention will now be described in further detail with reference to the accompanying drawings, which are simplified schematic diagrams that illustrate the basic structure of the present invention in a schematic manner.

[0044] In the description of the present invention, it should be understood that the terms "center", "longitudinal", "lateral", "length", "width", "thickness", "up", "down", "front", "back", "left", "right", "vertical", "horizontal", "top", "bottom", "inside", "outside", "clockwise", "counterclockwise", "axial", "radial", "circumferential" and the like indicate orientations or positional relationships based on the orientations or positional relationships shown in the accompanying drawings, and are only for the convenience of describing the present invention and simplifying the description, rather than indicating or implying that the device or element referred to must have a specific orientation, be constructed and operated in a specific orientation, and therefore cannot be understood as limiting the present invention. In addition, features defined as "first" or "second" may explicitly or implicitly include one or more of such features. In the description of the present invention, unless otherwise specified, "multiple" means two or more.

[0045] In the description of the present invention, it should be noted that, unless otherwise expressly specified or limited, the terms "mounted," "connected," and "connected" should be understood in a broad sense. For example, they may refer to fixed, detachable, or integral connections; mechanical or electrical connections; direct or indirect connections through an intermediate medium; and internal communication between two components. Those skilled in the art will understand the specific meanings of the above terms in the present invention based on the specific circumstances.

[0046] like Figure 1 As shown in FIG. 1 , the optimal embodiment of the present invention is a method for simulating asphaltene molecular dynamics behavior based on multi-software collaboration, which specifically includes the following steps:

[0047] (1) Drawing molecular models:

[0048] Four molecular models were constructed using the sketch tool of Materials Studio software, and then the clean tool of Materials Studio software was used to optimize the structure of each molecular model to eliminate unreasonable configurations in the bond lengths, bond angles, and dihedral angles of the molecular models.

[0049] Among them, the four molecular models are saturated hydrocarbon molecular model, aromatic hydrocarbon molecular model, colloid molecular model and asphaltene molecular model; further, saturated hydrocarbons include hexane, heptane, octane and wax molecules; aromatic hydrocarbons include benzene and toluene.

[0050] (2) Molecular force field file:

[0051] Each molecular model file was converted to .mol2 format, and a Python script was used to generate a topology file for use with the GROMACS program. The atomic RESP charges in each molecular model were then calculated and verified using Multiwfn software. Compared to existing methods for calculating atomic charges in topology files using Python scripts, the atomic RESP charges calculated using Multiwfn software are more accurate and reliable, improving the accuracy and reliability of the simulation. Furthermore, this calculation verification allows for checking the accuracy of the atomic RESP charges in the topology file, allowing for the timely identification and correction of potential problems.

[0052] Furthermore, the Python script can automatically call Antechamber in Ambertools to generate topology files.

[0053] (III) Construction of crude oil simulation system based on dynamic modeling method of topological relationship:

[0054] In Packmol software, first construct 8×8×8nm 3 The simulation box is divided into multiple sub-regions according to the topological relationship between each molecular model; saturated hydrocarbon molecular models, aromatic hydrocarbon molecular models, colloidal molecular models, and asphaltene molecular models are sequentially added to the sub-regions, and the size and shape of each sub-region are dynamically adjusted to accommodate the interactions between each molecular model to obtain a crude oil simulation system; in the GROMACS software, the steepest descent method is used to perform an energy minimization procedure on the crude oil simulation system to obtain an initial equilibrium system;

[0055] In this embodiment, the size and shape of each sub-region are dynamically adjusted, and the conformation of the molecule is appropriately adjusted to better adapt to the interaction between the molecular models. Each sub-region is dynamically adjusted, and this adjustment process can be achieved by changing the conformation of the molecule, twisting the bond angle, stretching the bond length, etc. Finally, the adjusted sub-regions are combined to obtain the crude oil simulation system. In the GROMACS software, the steepest descent method is used to perform the energy minimization program, where the temperature is set to 353K, the pressure is set to 0.1MPa, the time step is set to 2fs, and the number of steps is set to 5000000 steps. Then a simulation of 10ns is performed to obtain the initial equilibrium system of the crude oil simulation system. The simulation system construction process is as follows: Figure 3 shown.

[0056] It should be noted that topological modeling involves dividing the space into multiple regions and dynamically adjusting each subregion. By dividing the simulation box space into multiple subregions, this dynamic modeling approach allows for a more accurate description of the interactions between the molecular models, thereby improving the accuracy of the crude oil simulation results. Furthermore, by dynamically adjusting the size and shape of the subregions, unnecessary overlap and defects between molecules can be avoided during the simulation.

[0057] In this example, the asphaltene concentration is 10% to restore the real crude oil composition as much as possible.

[0058] like Figure 3 As shown, the number of the multiple sub-regions is eight, and sequentially adding the saturated hydrocarbon molecular model, the aromatic hydrocarbon molecular model, the colloid molecular model, and the asphaltene molecular model to the sub-regions specifically includes the following steps:

[0059] Saturated hydrocarbon molecular models are placed in all sub-regions to simulate the situation where saturated hydrocarbon molecular models exist in the simulation box;

[0060] The aromatic hydrocarbon molecule model is placed in the sub-region of the first half along the x, y, and z axes, where the first half is region A, to simulate the situation where the aromatic hydrocarbon molecule mainly exists in the surface layer.

[0061] The colloid molecule model is placed in the sub-region of the latter half along the x, y, and z axes, where the latter half is region B, to simulate the situation where it mainly exists in the deep layer;

[0062] Asphaltene molecular models are placed in all sub-regions to simulate the situation where the asphaltene molecular models are widely present in the entire simulation box.

[0063] (IV) Molecular dynamics simulation:

[0064] In GROMACS software, the initial equilibrium system was subjected to molecular dynamics simulation at a rate of not less than 30 ns to obtain the trajectory file of molecular motion;

[0065] The molecular dynamics simulation parameters were set to the NPT ensemble. The V-rescale method was used for temperature control during the molecular dynamics simulation, and the Berendsen method was used for pressure control. The initial velocity of each molecular model in the crude oil simulation system satisfied the Maxwell-Boltzmann distribution law. The GAFF force field was used to set the crude oil to extend infinitely in the x, y, and z directions, and periodic boundary conditions were used in each direction to avoid boundary effects caused by the limited size of the simulation box. The PME algorithm was used to calculate the long-range Coulomb interaction, and the cutoff radius of the short-range van der Waals interaction and Coulomb interaction was set to The LINCS algorithm is used to constrain all hydrogen bonds. In this embodiment, different crude oil system models are realized by setting different temperature, pressure conditions and different solvent compositions, which has a wide range of applications.

[0066] Taking temperature change as an example to further illustrate an embodiment of the present invention, the V-rescale method is used to control the temperature during the molecular dynamics simulation, and the cooling process of the initial equilibrium system is simulated, with the cooling rates of 2 K / ns, 1 K / ns, 0.8 K / ns and 0.4 K / ns respectively from 353 K to 293 K. The four rates are used for molecular dynamics simulations of 30 ns, 60 ns, 75 ns and 150 ns, respectively, to obtain trajectory files of molecular motion.

[0067] (V) Analysis of simulation results:

[0068] The temporal evolution of molecular motion trajectory files was observed using visual molecular dynamics software, and the dynamic characteristics of the trajectory files were analyzed using GROMACS software's built-in analysis tools, including radial distribution function, root mean square displacement, self-diffusion coefficient, cluster number, and hydrogen bond number.

[0069] Taking temperature change as an example, the trajectory files of molecular motion were processed. Specifically, the evolution of molecular configuration over time was observed by using Visual Molecular Dynamics (VMD) software. The four cooling rates of 2K / ns, 1K / ns, 0.8K / ns, and 0.4K / ns corresponded to the final aggregation states of asphaltene molecules in each system. Figure 4 As shown, the solvent molecules are hidden to facilitate the observation of the asphaltene aggregation state. It can be seen that a too fast cooling rate will cause the asphaltene clusters in the crude oil system to be smaller and more dispersed, while the slower the cooling rate, the fewer the asphaltene clusters, the larger the size, and the higher the degree of aggregation of the asphaltene molecules.

[0070] The radial distribution function between the centers of mass of asphaltene molecules at four cooling rates was calculated using the radial distribution function analysis tool built into the GROMACS software. Figure 5 As shown in the figure, the first peak of g(r) appears around 0.38 nm, indicating that the distance between adjacent molecules in the asphaltene clusters is approximately 0.38 nm. The peak of g(r) increases with decreasing cooling rate, indicating that slower cooling rates in crude oil systems increase the degree of asphaltene aggregation. Consequently, the number of asphaltene clusters decreases while their size increases.

[0071] In this embodiment, the analysis process of the influence of other factors such as different pressure conditions, different asphaltene structures, and different solvent compositions on the degree of asphaltene aggregation is consistent with the analysis process of the influence of temperature changes on the degree of asphaltene aggregation in this embodiment. For the sake of brevity, they will not be repeated here.

[0072] It should be noted that the present invention makes full use of the combination of various molecular dynamics software to realize the simulation of asphaltene. Technically speaking, it requires certain technical means to connect the output files of different software together. At the same time, the input and output formats of different software may be different, and format conversion is required. In addition, there are differences in the parameter settings and calculation methods of different software, which need to be optimized and adjusted. In order to overcome these technical difficulties, for example, the molecular model file drawn and optimized by Materials Studio software in this application needs to be output as a .mol2 file that can be calculated by Python script, and a topology file is generated by Python script, and Multiwfn software is used to calculate the atomic charges of each molecular model to replace the atomic charges in the topology file, etc., thereby improving the accuracy of molecular dynamics simulation, better simulating the dynamic changes between molecules, improving the accuracy and credibility of the simulation, improving the simulation efficiency, and solving the functional limitations of using a single software.

[0073] The asphaltene molecular dynamics behavior simulation method based on multi-software collaboration of the present invention solves the difficult problems that cannot be solved in experiments and explores the aggregation behavior of asphaltene molecules at the nanoscale; by constructing a crude oil simulation system through a dynamic modeling method based on topological relationships, the dynamic changes between molecules can be better simulated, avoiding the limitations of the static modeling method of fixing the molecular structure, thereby improving the accuracy and credibility of the simulation; the scope of application is wide, and it is applicable to any asphaltene molecular structure model, and crude oil system models with different temperature, pressure conditions and different solvent compositions can be set according to needs; the advantages of various molecular dynamics software are fully utilized. Materials Studio software can visually draw molecular models and realize molecular configuration optimization. Python scripts can automatically generate molecular topology files. Packmol software can arbitrarily stack specified molecules into specified areas according to custom rules. GROMACS software has fast calculation speed and high parallel efficiency.

[0074] With the above-described preferred embodiments of the present invention as a guide, and with reference to the above description, relevant personnel are fully capable of making various changes and modifications without departing from the technical scope of this invention. The technical scope of this invention is not limited to the contents of the specification and must be determined according to the scope of the claims.

Claims

1. A method for simulating asphaltene molecular dynamics behavior based on multi-software collaboration, characterized in that: The specific steps include: (1) Drawing molecular models: Using the sketch tool of Materials Studio software to construct four molecular models, and then using the clean tool of the Materials Studio software to optimize the structure of each molecular model; Among them, the four molecular models are saturated hydrocarbon molecular model, aromatic hydrocarbon molecular model, colloid molecular model and asphaltene molecular model; (2) Obtaining molecular force field files: Each molecular model file is converted to .mol2 format, a Python script is used to calculate and generate a topology file that can be used by the GROMACS program, and the atomic RESP charges in each molecular model are calculated and verified by the Multiwfn software; (III) Construction of crude oil simulation system based on dynamic modeling method of topological relationship: In Packmol software, first construct 8×8×8nm 3 A simulation box, dividing the simulation box into multiple sub-areas according to the topological relationship between each of the molecular models; sequentially adding the saturated hydrocarbon molecular model, the aromatic hydrocarbon molecular model, the colloid molecular model, and the asphaltene molecular model into the sub-regions, dynamically adjusting the size and shape of each sub-region to accommodate the interaction between each molecular model, and obtaining the crude oil simulation system; In GROMACS software, the crude oil simulation system is subjected to an energy minimization program using the steepest descent method to obtain an initial equilibrium system; (IV) Molecular dynamics simulation: In GROMACS software, the initial equilibrium system is subjected to molecular dynamics simulation at a rate of not less than 30 ns to obtain a trajectory file of molecular motion; (V) Analysis of simulation results: The evolution of the trajectory file of the molecular motion over time was observed by visual molecular dynamics software, and the dynamic characteristics of the trajectory file of the molecular motion were analyzed by the built-in analysis tool of the GROMACS software.

2. The asphaltene molecular dynamics behavior simulation method based on multi-software collaboration as claimed in claim 1, characterized in that: The saturated hydrocarbons include hexane, heptane, octane and wax molecules; The aromatic hydrocarbons include benzene and toluene.

3. The asphaltene molecular dynamics behavior simulation method based on multi-software collaboration as claimed in claim 1, characterized in that: The Python script can automatically call Antechamber in Ambertools to generate the topology file.

4. The asphaltene molecular dynamics behavior simulation method based on multi-software collaboration as claimed in claim 1, characterized in that: The number of the multiple sub-regions is eight, and sequentially adding the saturated hydrocarbon molecular model, the aromatic hydrocarbon molecular model, the colloid molecular model, and the asphaltene molecular model to the sub-regions specifically includes the following steps: placing the saturated hydrocarbon molecular model into all sub-regions to simulate the situation where the saturated hydrocarbon molecular model exists in the simulation box; placing the aromatic hydrocarbon molecule model into the sub-region of the front half along the x, y, and z axes to simulate the situation where the aromatic hydrocarbon molecule mainly exists in the surface layer; The colloid molecule model is placed in the sub-region of the latter half along the x, y, and z axes to simulate the situation that it mainly exists in the deep layer; The asphaltene molecular model is placed in all sub-regions to simulate the situation where the asphaltene molecular model widely exists in the entire simulation box.

5. The asphaltene molecular dynamics behavior simulation method based on multi-software collaboration as claimed in claim 1, characterized in that: The molecular dynamics simulation parameters are NPT ensemble.

6. The asphaltene molecular dynamics behavior simulation method based on multi-software collaboration as claimed in claim 5, characterized in that: The temperature control during the molecular dynamics simulation was performed using the V-rescale method.

7. The asphaltene molecular dynamics behavior simulation method based on multi-software collaboration as claimed in claim 5, characterized in that: The Berendsen method was used for pressure control during the molecular dynamics simulation.

8. The asphaltene molecular dynamics behavior simulation method based on multi-software collaboration as claimed in claim 5, characterized in that: During the molecular dynamics simulation, the initial velocity of each molecular model in the crude oil simulation system satisfies the Maxwell-Boltzmann distribution law, and the crude oil is assumed to be infinitely extended in the x, y, and z directions using a GAFF force field, and periodic boundary conditions are used in each direction; The PME algorithm is used to calculate the long-range Coulomb interaction, and the cutoff radius of the short-range van der Waals interaction and Coulomb interaction is set to All hydrogen bonds were constrained using the LINCS algorithm.

9. The asphaltene molecular dynamics behavior simulation method based on multi-software collaboration as claimed in claim 1, characterized in that: The built-in analysis tools of the GROMACS software include radial distribution function, root mean square displacement, self-diffusion coefficient, cluster number and hydrogen bond number.

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