Molecular dynamics visualization method and system based on gridding water molecule density calculation

Abstract

The invention discloses a molecular dynamics visualization method and system based on gridding water molecule density calculation, and the method specifically comprises the steps: S1, obtaining a coordinate track file of water molecules in simulation operation time based on molecular dynamics simulation, and extracting the three-dimensional coordinate information of oxygen atoms in the water molecules based on the coordinate track file; s2, creating a three-dimensional space grid based on the three-dimensional coordinate information of the oxygen atoms, and acquiring the number of the oxygen atoms in the grid and the volume of each grid based on the three-dimensional space grid; s3, obtaining the number of water molecules based on the number of the oxygen atoms in the grids, calculating the density of the water molecules in the grids based on the number of the water molecules and the volume of each grid, and generating a two-dimensional density grid based on the density value of the water molecules in each grid; and S4, preprocessing the density data of the two-dimensional density grid, and then carrying out visual output to realize molecular dynamics visualization based on grid water molecule density calculation.

Description

Technical Field

[0001] The present invention relates to the technical field of molecular dynamics simulation, and in particular to a molecular dynamics visualization method and system based on gridded water molecule density calculation. Background Art

[0002] Existing molecular dynamics simulations are widely used to study the molecular adsorption and interaction processes at material interfaces. However, when visualizing and analyzing the simulation results, the following problems are prone to occur:

[0003] 1. Existing molecular visualization methods cannot clearly display the distribution state of water molecules, especially on high-density interfaces, which can easily lead to a chaotic display of water molecules and make it difficult to conduct accurate analysis. Existing molecular visualization software usually directly displays the specific location of water molecules in units of molecules, which often leads to a messy picture in areas with dense water molecules, making it difficult to clearly understand the distribution of water molecules on the interface. This method has particularly obvious limitations when studying the microstructure of the hydration layer or molecular adsorption on the interface, and it is difficult to determine the aggregation and diffusion state of water molecules on the interface.

[0004] 2. When studying the interface adsorption mechanism, it is difficult to accurately display the density and distribution of water molecules on the interface. The existing methods are not sufficient to intuitively reflect the aggregation areas and water-free areas of water molecules on the interface.

[0005] Therefore, developing a new method that can accurately display the density distribution of water molecules is crucial to improving the visualization and resolution of molecular dynamics simulations. Summary of the invention

[0006] In order to solve the above technical problems, the present invention provides a molecular dynamics visualization method based on gridded water molecule density calculation, the method comprising:

[0007] Step S1, based on molecular dynamics simulation, obtaining a coordinate trajectory file of a water molecule during the simulation running time, and extracting three-dimensional coordinate information of oxygen atoms in the water molecule based on the coordinate trajectory file;

[0008] Step S2, creating a three-dimensional space grid based on the three-dimensional coordinate information of the oxygen atoms, and obtaining the number of oxygen atoms in the grid and the volume of each grid based on the three-dimensional space grid;

[0009] Step S3, obtaining the number of water molecules based on the number of oxygen atoms in the grid, calculating the density of water molecules in the grid based on the number of water molecules and the volume of each grid, and generating a two-dimensional density grid based on the water molecule density value of each grid;

[0010] Step S4, pre-processing the density data of the two-dimensional density grid and then outputting the resultant density data to realize molecular dynamics visualization based on gridded water molecule density calculation.

[0011] Optionally, in step S1, the method for extracting the three-dimensional coordinate information of the oxygen atoms in the water molecules based on the coordinate trajectory file specifically includes:

[0012] Based on the PDB file in the coordinate trajectory file, use the read_pdb function to read the content of the PDB file;

[0013] The three-dimensional coordinates of oxygen atoms are obtained by scanning each line of data in the PDB file.

[0014] Optionally, in step S2, the process of calculating the volume of each grid specifically includes:

[0015] Creating a three-dimensional spatial grid based on the three-dimensional coordinates of the oxygen atoms and a preset grid resolution;

[0016] Compute the volume for each cell in a grid:

[0017] v = 5*5*(z_max-z_min)

[0018] Among them, z_max is the maximum z coordinate value of the oxygen atom in the saved PDB coordinate file, and z_min is the minimum z coordinate value of the oxygen atom in the saved water molecule PDB coordinate file.

[0019] Optionally, in step S3, the process of calculating the density of water molecules in the grid based on the number of water molecules in the grid and the volume of each grid specifically includes:

[0020] d = (OW quantity * 180) / 6.02 * v)

[0021] Here, OW is the number of oxygen atoms counted.

[0022] The present invention also discloses a molecular dynamics visualization system based on gridded water molecule density calculation, the system comprising: a molecular coordinate extraction module, a grid information extraction module, a grid density calculation module and a molecular visualization module;

[0023] The molecular coordinate extraction module is used to obtain the coordinate trajectory file of the water molecules within the simulation running time based on the molecular dynamics simulation, and extract the three-dimensional coordinate information of the oxygen atoms in the water molecules based on the coordinate trajectory file;

[0024] The grid information extraction module is used to create a three-dimensional space grid based on the three-dimensional coordinate information of the oxygen atoms, and obtain the number of oxygen atoms in the grid and the volume of each grid based on the three-dimensional space grid;

[0025] The grid density calculation module is used to obtain the number of water molecules based on the number of oxygen atoms in the grid, calculate the density of water molecules in the grid based on the number of water molecules and the volume of each grid, and generate a two-dimensional density grid based on the water molecule density value of each grid;

[0026] The grid density calculation module is used to pre-process the density data of the two-dimensional density grid and then output it visually, so as to realize molecular dynamics visualization based on gridded water molecule density calculation.

[0027] Optionally, in the molecular coordinate extraction module, the method for extracting the three-dimensional coordinate information of the oxygen atoms in the water molecules based on the coordinate trajectory file specifically includes:

[0028] Based on the PDB file in the coordinate trajectory file, use the read_pdb function to read the content of the PDB file;

[0029] The three-dimensional coordinates of oxygen atoms are obtained by scanning each line of data in the PDB file.

[0030] Optionally, in the grid information extraction module, the process of calculating the volume of each grid specifically includes:

[0031] Creating a three-dimensional spatial grid based on the three-dimensional coordinates of the oxygen atoms and a preset grid resolution;

[0032] Compute the volume for each cell in a grid:

[0033] v = 5*5*(z_max-z_min)

[0034] Among them, z_max is the maximum z coordinate value of the oxygen atom in the saved PDB coordinate file, and z_min is the minimum z coordinate value of the oxygen atom in the saved water molecule PDB coordinate file.

[0035] Optionally, in the grid density calculation module, the process of calculating the density of water molecules in the grid based on the number of water molecules in the grid and the volume of each grid specifically includes:

[0036] d = (OW quantity * 180) / 6.02 * v)

[0037] Here, OW is the number of oxygen atoms counted.

[0038] Compared with the prior art, the present invention has the following beneficial effects:

[0039] The present invention can read molecular structure data files, extract the spatial coordinates of specific molecules, construct a three-dimensional space grid according to a certain resolution, calculate the density of molecules in different grid areas, and output the corresponding two-dimensional density map. Through this tool, researchers can easily visualize molecular density, which can be used for data analysis and research in the fields of materials science and biochemistry. The present invention can accurately display the aggregation and sparse areas of water molecules on the interface by spatially partitioning water molecules and calculating the density of each area, which is more intuitive than traditional molecular visualization methods. This method can better display the thickness and uniformity of the hydration layer, helping researchers understand the dynamic behavior of water molecules under different conditions, and the interaction with other molecules. This method is suitable for interfacial adsorption research in multiple fields such as materials science, biomedicine, and chemistry, and has important application value in particular in the study of water molecule behavior, such as protein adsorption, surface modification of nanomaterials, etc. BRIEF DESCRIPTION OF THE DRAWINGS

[0040] In order to more clearly illustrate the technical solution of the present invention, the following briefly introduces the drawings required for use in the embodiments. Obviously, the drawings described below are only some embodiments of the present invention. For ordinary technicians in this field, other drawings can be obtained based on these drawings without paying creative labor.

[0041] Figure 1 A method step diagram of a molecular dynamics visualization method according to an embodiment of the present invention;

[0042] Figure 2 The density distribution of water molecules within 7 angstroms from the surface at different times is displayed by the molecular dynamics visualization method based on gridded water molecule density calculation in the embodiment of the present invention. Figure (a) shows the density distribution of water molecules within 7 angstroms from the surface at 19.5 ns; Figure (b) shows the density distribution of water molecules within 7 angstroms from the surface at 21.1 ns; Figure (c) shows the density distribution of water molecules within 7 angstroms from the surface at 40.8 ns; Figure (d) shows the density distribution of water molecules within 7 angstroms from the surface at 50 ns.

[0043] Figure 3 This is a data format diagram of the PDB file of water molecule coordinates according to an embodiment of the present invention. Specific implementation methods

[0045] The following will be combined with the drawings in the embodiments of the present invention to clearly and completely describe the technical solutions in the embodiments of the present invention. Obviously, the described embodiments are only part of the embodiments of the present invention, rather than all the embodiments. Based on the embodiments in the present invention, all other embodiments obtained by ordinary technicians in this field without creative work are within the scope of protection of the present invention. In order to make the above-mentioned purposes, features and advantages of the present invention more obvious and easy to understand, the present invention is further described in detail below in combination with the drawings and specific embodiments.

[0046] Embodiment 1

[0047] A molecular dynamics visualization method based on gridded water molecule density calculation, such as Figure 1 As shown, specifically including:

[0048] Step S1, based on molecular dynamics simulation, obtaining a coordinate trajectory file of a water molecule during the simulation running time, and extracting three-dimensional coordinate information of oxygen atoms in the water molecule based on the coordinate trajectory file.

[0049] First, through molecular dynamics simulation, the motion trajectory and spatial position data of water molecules above the target interface are obtained. In this example, the target interface is graphite. After running the molecular dynamics, the coordinate trajectory file within the running time is obtained. A frame of the PDB file at the time you want to observe is selected, and only the coordinates of the water molecules within 7 angstroms above the first layer of the interface are saved. Through the read_pdb() function, the program first reads the contents of the PDB file and extracts the three-dimensional coordinates (x, y, z) of all oxygen atoms (the element name is "OW"). This operation is achieved by scanning each line of data, such as Figure 3As shown, the 13th to 16th columns in the PDB coordinate file are element names, the 31st to 38th columns are x coordinates, the 39th to 46th columns are y coordinates, and the 47th to 54th columns are z coordinates. All qualified oxygen atom coordinates are stored in an array for subsequent use. Through molecular dynamics simulation, the motion trajectory file of water molecules during the simulation run is obtained, and the three-dimensional coordinate information of oxygen atoms in water molecules is extracted therefrom. Molecular dynamics simulation is a computer simulation technology used to study the motion behavior of molecules under specific environments. In this simulation, we use Gromacs software to simulate the adsorption process of mussel foot silk protein (Mfp-5) on the graphite surface. The simulation environment is an NVT system, i.e., the conditions of fixed particle number, fixed volume and fixed temperature, ensuring that the system runs at a constant temperature (300K), similar to observing material changes in a constant temperature room. In order to accurately describe the interaction between protein and water molecules, the present invention uses the AMBER force field to process the molecular behavior of protein, and water molecules use the TIP3P model. Long-range electrostatic interactions are processed by the particle mesh Ewald (PME) method. In order to simulate the kinetics of protein adsorption on the graphite surface, the graphite surface was represented by sp 2 The hybridized carbon atoms consist of uncharged and immobile sheets with a C-C bond length of 1.42 Å to match experimental observations. The interactions between carbon atoms in graphite and atoms in proteins are represented by Lennard-Jones (LJ) potentials. The dimensions of the simulation box are 9.80 × 9.35 × 10.00 nm. 3 , and periodic boundary conditions are applied in three directions. First, the water molecules are relaxed for energy minimization using the steepest descent method. Next, a 100ps MD simulation is performed to equilibrate the water molecules while restraining the protein backbone atoms. Subsequently, an unrestrained production run of 50ns is performed with a time step of 1fs. During the simulation, the position change information of the water molecules (three-dimensional coordinates of oxygen atoms and hydrogen atoms) is recorded, and these data are used to analyze how the protein affects the distribution of water molecules when adsorbed on the graphite surface. We will save the water molecules within 7 angstroms above the first layer interface into a coordinate file (PDB file) for further analysis.

[0050] In molecular dynamics simulations, the hydration layer changes over time. By analyzing the coordinate data of water molecules at multiple time points, we can deeply study the dynamic behavior of water molecules. Previous studies have shown that water molecules at the interface usually form up to two ordered hydration layers in the direction of the surface normal, that is, within 7 angstroms above the first layer interface. Therefore, we will save the water molecules within 7 angstroms above the first layer interface into the coordinate file (PDB file) for further analysis.

[0051] Step S2, create a three-dimensional space grid based on the three-dimensional coordinate information of the oxygen atom, and obtain the number of oxygen atoms in the grid and the volume of each grid based on the three-dimensional space grid. According to the data of all the rows of OW elements read, that is, the rows of oxygen atoms, the number of times oxygen atoms appear, that is, the number of oxygen atoms, can be counted within each grid range according to the coordinates of oxygen atoms. Since a water molecule contains an oxygen atom and two hydrogen atoms, as long as the number of oxygen atoms in each grid is counted, the number of water molecules in each grid and the volume of each grid can be represented. The interface area is divided into several small grids (or voxels), and the size of each grid is adjusted as needed, generally selecting 3 angstroms to 7 angstroms to ensure the accuracy of density distribution. In each grid, the number of water molecules in a specific time period at a selected time is counted. The specific time period referred to in this embodiment is when the protein just contacts the interface, the partial structure of the protein is adsorbed on the interface, and the protein is completely adsorbed on the interface, when the changes in the arrangement of water molecules occur, and the water molecule density in the area is calculated according to the volume, and converted to finally form water molecule density distribution data.

[0052] The create_grid() function takes the extracted OW atomic coordinates and creates a 3D grid based on the user-defined grid resolution (5 angstroms in the x and y directions, and the z-axis is automatically set based on the z-coordinate difference of the PDB data). In this case, the maximum x and y values ​​of the entire interface are 98 angstroms and 93 angstroms, respectively.

[0053] The grid resolution of the x-axis and y-axis can usually be fixed to 3 Å to 7 Å (set to 5 Å in this case), while the resolution of the z-axis is dynamically determined based on the difference between the maximum and minimum values ​​of the extracted z-coordinates.

[0054] The program assigns each OW atom to the corresponding grid according to its coordinates and counts the number of oxygen atoms in each grid. In addition, this step calculates the volume of each grid using the formula v = 5*5*(z_max-z_min) in cubic angstroms.

[0055] In molecular dynamics simulations, the hydration layer evolves over time. By analyzing data at multiple time points, we can study the dynamic behavior of water molecules. Previous studies have shown that water molecules at the interface usually form at most two ordered hydration layers along the surface normal direction; therefore, the image focuses on the distribution of water molecules within 7 angstroms above the first interface, corresponding to the area of ​​these two hydration layers. Therefore, in this case, in the z direction, only water molecules within 7 angstroms above the first interface are extracted for collection.

[0056] Step S3, based on the number of oxygen atoms in the grid, the number of water molecules is obtained, based on the number of water molecules and the volume of each grid, the density of water molecules in the grid is calculated, and a two-dimensional density grid is generated based on the water molecule density value of each grid. The density of water molecules is displayed by changing the color or transparency, and the high-density area is displayed as a dark color or low transparency, and the low-density or water-free area is displayed as a light color or high transparency, so as to generate a visual density distribution map.

[0057] The density is calculated based on the number of OW atoms in the grid, with the formula d = (number of OW*180) / 6.02*v), where v is the volume of each grid and the number of OW atoms is the number of atoms in each grid.

[0058] Finally, a two-dimensional density grid containing the density values ​​of each grid area is generated and is ready for subsequent visualization output.

[0059] Step S4: pre-process the density data of the two-dimensional density grid and then output it for visualization, so as to realize molecular dynamics visualization based on gridded water molecule density calculation. Figure 2 As shown in (a)-(d), the density map can be used to intuitively analyze the distribution of water molecules on the interface, and to clarify which areas have dense water molecules and which areas have fewer or no water molecules. The method provided by the present invention is particularly suitable for analyzing the formation of an interfacial hydration layer and the adsorption behavior of proteins on the interface.

[0060] Through the plot_density_clipped() function, the system visualizes the generated density grid.

[0061] The density data is smoothed using an interpolation algorithm, making the output image smoother and more natural, making it easier to observe the density distribution trend.

[0062] The system uses the matplotlib library to generate high-resolution contour fill maps, and uses the Times New Roman font to ensure the professionalism and aesthetics of the image.

[0063] Finally, the program saves the generated image as a high-resolution picture and outputs it to the specified path for further use or publication.

[0064] Embodiment 2

[0065] A molecular dynamics visualization system based on gridded water molecule density calculation, the system comprising: a molecular coordinate extraction module, a grid information extraction module, a grid density calculation module and a molecular visualization module;

[0066] The molecular coordinate extraction module is used to obtain the coordinate trajectory file of the water molecule during the simulation running time based on the molecular dynamics simulation, and extract the three-dimensional coordinate information of the oxygen atom in the water molecule based on the coordinate trajectory file.

[0067] First, the motion trajectory and spatial position data of water molecules above the target interface are obtained through molecular dynamics simulation. After running the molecular dynamics, the coordinate trajectory file during the running time is obtained. A frame of PDB file at the time you want to observe is selected. Through the read_pdb() function, the program first reads the content of the PDB file and extracts the three-dimensional coordinates (x, y, z) of all oxygen atoms (element name "OW"). This operation is achieved by scanning each line of data, such as Figure 3 As shown, columns 13-16 in the PDB coordinate file are element names, columns 31-38 are x-coordinates, columns 39-46 are y-coordinates, and columns 47-54 are z-coordinates. All oxygen atom coordinates that meet the conditions are stored in an array for subsequent use.

[0068] The grid information extraction module is used to create a three-dimensional space grid based on the three-dimensional coordinate information of the oxygen atoms, and obtain the number of oxygen atoms in the grid and the volume of each grid based on the three-dimensional space grid.

[0069] The create_grid() function takes the extracted OW atomic coordinates and creates a 3D grid based on the user-defined grid resolution (5 angstroms in the x and y directions, and the z-axis is automatically set based on the z-coordinate difference of the PDB data). In this case, the maximum x and y values ​​of the entire interface are 98 angstroms and 93 angstroms, respectively.

[0070] The grid resolution of the x-axis and y-axis can usually be fixed to 3 angstroms to 7 angstroms (in this case, it is set to ), and the resolution of the z-axis is dynamically determined based on the difference between the maximum and minimum values ​​of the extracted z-coordinates.

[0071] The program assigns each OW atom to the corresponding grid according to its coordinates and counts the number of molecules in each grid. In addition, this step calculates the volume of each grid using the formula v = 5*5*(z_max-z_min) in cubic angstroms.

[0072] In molecular dynamics simulations, the hydration layer evolves over time. By analyzing data at multiple time points, we can study the dynamic behavior of water molecules. Previous studies have shown that water molecules at the interface usually form at most two ordered hydration layers along the surface normal direction; therefore, the image focuses on the distribution of water molecules within 7 angstroms from the first interface, corresponding to the area of ​​these two hydration layers. Therefore, in this case, in the z direction, only water molecules within 7 angstroms above the first interface are extracted for collection.

[0073] The grid density calculation module is used to obtain the number of water molecules based on the number of oxygen atoms in the grid, calculate the water molecule density in the grid based on the number of water molecules and the volume of each grid, and generate a two-dimensional density grid based on the water molecule density value of each grid.

[0074] The density is calculated based on the number of OW atoms in the grid, with the formula d = (number of OW*180) / 6.02*v), where v is the volume of each grid and the number of OW atoms is the number of molecules in each grid.

[0075] Finally, a two-dimensional density grid containing the density values ​​of each grid area is generated and is ready for subsequent visualization output.

[0076] The molecular visualization module is used to pre-process the density data of the two-dimensional density grid and then perform visualization output to achieve molecular dynamics visualization based on gridded water molecule density calculation.

[0077] Through the plot_density_clipped() function, the system visualizes the generated density grid.

[0078] The density data is smoothed using an interpolation algorithm, making the output image smoother and more natural, making it easier to observe the density distribution trend.

[0079] The system uses the matplotlib library to generate high-resolution contour fill maps, and uses the Times New Roman font to ensure the professionalism and aesthetics of the image.

[0080] Finally, the program saves the generated image as a high-resolution picture and outputs it to the specified path for further use or publication.

[0081] Embodiment 3

[0082] All molecular dynamics (MD) simulations were performed using Gromacs 5.1.4 software under the NVT ensemble. The marine mussel Mfp-5 protein was simulated using the AMBER force field, and the TIP3P model was used for the explicit water solvent. The Mfp-5 protein was placed in a cubic simulation box containing 10,789 water molecules. The MD integration time step was set to 1.0 fs, and MD snapshots were saved every 20 ps. Long-range electrostatic interactions were treated by the particle mesh Ewald (PME) method with a cutoff distance of 1.2 nm. Short-range van der Waals (VDW) interactions were also cutoff at 1.2 nm. The temperature was controlled by a V-rescale thermostat to keep the system at 1 bar and 300 K with a relaxation time of 0.1 ps. The LINCS algorithm was used to constrain all bonds involving hydrogen atoms.

[0083] In order to simulate the kinetics of protein adsorption on the graphite surface, the graphite surface was represented by sp 2 Hybridized carbon atoms consist of uncharged and immobile sheets with a C-C bond length of 1.42 Å to match experimental observations. The interactions between carbon atoms in graphite and atoms in proteins are represented by Lennard-Jones (LJ) potentials. The dimensions of the simulation box are 9.80 × 9.35 × 10.00 nm. 3 , and periodic boundary conditions were applied in three directions. First, the water molecules were relaxed for energy minimization using the steepest descent method. Next, 100 ps of MD simulations were performed to equilibrate the water molecules while restraining the protein backbone atoms. Subsequently, 50 ns of unconstrained production runs were performed with a time step of 1 fs. The MD simulation results were visualized using PyMol and Visual Molecular Dynamics (VMD) software.

[0084] Structural prediction of Mfp-5: The amino acid sequence of Mfp-5 is: SSEEYKGGYYPGNAYHYHSGGSYHGSGYHGGYKGKYYGKAKKYYYKYKNSGKYKYLKKARKYHRKGYK YYGGSS. The conformational dynamics of Mfp-5 were studied by using the REMD (Replica Exchange Molecular Dynamics) method. The REMD simulation used 60 replicas with a temperature range of 300K to 506.5K and a temperature interval of 3.5K between adjacent replicas. This temperature range and distribution were determined by preliminary tests to optimize the exchange efficiency between replicas. Mfp-5 was placed in a cubic simulation box and dissolved in 10,789 water molecules. The system was first equilibrated for 200ps using the NPT ensemble at 300K and 1bar pressure to achieve the correct density and distribution of water molecules. The equilibrated system was used as the initial configuration for all replicas in the REMD simulation.

[0085] After initial equilibration, each replica was briefly pre-simulated under the NVT ensemble to adjust the system to its assigned temperature. This step ensured that each replica reached thermal equilibrium before the production phase of the REMD simulation. Subsequently, each replica was simulated under NVT ensemble conditions for 30 ns, with replica swaps attempted every 2 ps, with the swap frequency chosen to balance the need for computational efficiency and adequate sampling. Although each replica was simulated for 30 ns, only the last 20 ns of data were used for analysis. This approach allowed the system to reach equilibrium, minimizing the impact of initial conditions on the results.

[0086] The structure of the protein was generated using AMBER force field parameters. The tyrosine residues of Mfp-5 were post-translationally modified by the addition of hydroxyl groups to generate DOPA residues as previously described in the literature. The charge parameters of DOPA were obtained from the AMBER General Force Field (GAFF), while the bond, angle, dihedral and LJ parameters were directly adopted from the AMBER force field. This refined parameterization was essential to accurately capture the chemical properties of the DOPA-modified Mfp-5 protein. We performed conformational clustering analysis using the g_cluster tool in GROMACS with an RMSD cutoff of 0.9 nm. The most representative clusters were identified as representative structures and further analyzed for the adhesion mechanism of Mfp-5.

[0087] The experimental results are as follows: In the molecular dynamics simulation, the hydration layer evolves over time. By analyzing the data at multiple time points, we can study the dynamic behavior of water molecules. To this end, we used Python's Matplotlib library to create a two-dimensional density map of water molecules. Each grid in the density map represents the relative density of water molecules, with blue areas representing high density and white areas representing low density or water-free areas. This resolution enables the image to clearly show the dehydration transition of water molecules over time. By observation, we found that adsorption gradually occurred as the dehydrated area began to expand. The depletion of water molecules is usually associated with a dehydration transition triggered by a restrictive interaction between two hydrophobic surfaces. This way of displaying the water molecule density grid can better explain why the adhesion strength of proteins at the interface is enhanced.

[0088] The embodiments described above are only descriptions of the preferred embodiments of the present invention and are not intended to limit the scope of the present invention. Without departing from the design spirit of the present invention, various modifications and improvements made to the technical solutions of the present invention by ordinary technicians in this field should all fall within the protection scope determined by the claims of the present invention.

Claims

1. A molecular dynamics visualization method based on gridded water molecule density calculation, characterized in that: The method comprises: Step S1, based on molecular dynamics simulation, obtaining a coordinate trajectory file of a water molecule during the simulation running time, and extracting three-dimensional coordinate information of oxygen atoms in the water molecule based on the coordinate trajectory file; Step S2, creating a three-dimensional space grid based on the three-dimensional coordinate information of the oxygen atoms, and obtaining the number of oxygen atoms in the grid and the volume of each grid based on the three-dimensional space grid; Step S3, obtaining the number of water molecules based on the number of oxygen atoms in the grid, calculating the density of water molecules in the grid based on the number of water molecules and the volume of each grid, and generating a two-dimensional density grid based on the water molecule density value of each grid; Step S4, preprocessing the density data of the two-dimensional density grid and then outputting the resultant density data to realize molecular dynamics visualization based on gridded water molecule density calculation.

2. The molecular dynamics visualization method based on gridded water molecule density calculation according to claim 1, characterized in that: In step S1, the method for extracting the three-dimensional coordinate information of oxygen atoms in water molecules based on the coordinate trajectory file specifically includes: Based on the PDB file in the coordinate trajectory file, use the read_pdb function to read the content of the PDB file; The three-dimensional coordinates of oxygen atoms are obtained by scanning each line of data in the PDB file.

3. The molecular dynamics visualization method based on gridded water molecule density calculation according to claim 1, characterized in that: In step S2, the process of calculating the volume of each grid specifically includes: Creating a three-dimensional spatial grid based on the three-dimensional coordinates of the oxygen atoms and a preset grid resolution; Compute the volume for each cell in a grid: v = 5*5*(z_max-z_min) Among them, z_max is the maximum z coordinate value of the oxygen atom in the saved PDB coordinate file, and z_min is the minimum z coordinate value of the oxygen atom in the saved water molecule PDB coordinate file.

4. The molecular dynamics visualization method based on gridded water molecule density calculation according to claim 1, characterized in that: In step S3, the process of calculating the density of water molecules in the grid based on the number of water molecules in the grid and the volume of each grid specifically includes: d = (OW quantity * 180) / 6.02 * v) Here, OW is the number of oxygen atoms counted.

5. A molecular dynamics visualization system based on gridded water molecule density calculation, the visualization system is used to implement the visualization method according to any one of claims 1 to 4, characterized in that: The system comprises: a molecular coordinate extraction module, a grid information extraction module, a grid density calculation module and a molecular visualization module; The molecular coordinate extraction module is used to obtain the coordinate trajectory file of the water molecules within the simulation running time based on the molecular dynamics simulation, and extract the three-dimensional coordinate information of the oxygen atoms in the water molecules based on the coordinate trajectory file; The grid information extraction module is used to create a three-dimensional space grid based on the three-dimensional coordinate information of the oxygen atoms, and obtain the number of oxygen atoms in the grid and the volume of each grid based on the three-dimensional space grid; The grid density calculation module is used to obtain the number of water molecules based on the number of oxygen atoms in the grid, calculate the density of water molecules in the grid based on the number of water molecules and the volume of each grid, and generate a two-dimensional density grid based on the water molecule density value of each grid; The grid density calculation module is used to pre-process the density data of the two-dimensional density grid and then output it visually, so as to realize molecular dynamics visualization based on gridded water molecule density calculation.

6. The molecular dynamics visualization system based on gridded water molecule density calculation according to claim 5, characterized in that: In the molecular coordinate extraction module, the method for extracting the three-dimensional coordinate information of oxygen atoms in water molecules based on the coordinate trajectory file specifically includes: Based on the PDB file in the coordinate trajectory file, use the read_pdb function to read the content of the PDB file; The three-dimensional coordinates of oxygen atoms are obtained by scanning each line of data in the PDB file.

7. The molecular dynamics visualization system based on gridded water molecule density calculation according to claim 5, characterized in that: In the grid information extraction module, the process of calculating the volume of each grid specifically includes: Creating a three-dimensional spatial grid based on the three-dimensional coordinates of the oxygen atoms and a preset grid resolution; Compute the volume for each cell in a grid: v = 5*5*(z_max-z_min) Among them, z_max is the maximum z coordinate value of the oxygen atom in the saved PDB coordinate file, and z_min is the minimum z coordinate value of the oxygen atom in the saved water molecule PDB coordinate file.

8. The molecular dynamics visualization system based on gridded water molecule density calculation according to claim 5, characterized in that: In the grid density calculation module, the process of calculating the density of water molecules in the grid based on the number of water molecules in the grid and the volume of each grid specifically includes: d = (OW quantity * 180) / 6.02 * v) Here, OW is the number of oxygen atoms counted.

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