Method for determining anti-freezing property of pectin based on molecular dynamics simulation

Abstract

The invention discloses a method for determining the anti-freezing property of pectin based on molecular dynamics simulation, which comprises the following steps: constructing an ice layer and pectin structure, then constructing two structure files of the ice layer and pectin as well as water and pectin, merging to obtain a nucleation model system, and finally establishing a box for the system; performing energy minimization, undercooling, pressure control balance and simulation, and calculating an initial solid water molecule number N0; calculating the number NI and NII of solid and liquid water molecules after simulation to obtain a critical temperature TL; the method comprises the following steps: performing simulation under 1bar and different supercooling temperatures, outputting a structure file according to a simulated track file, respectively establishing solid and liquid water molecule index files, calculating free energy difference of solid and liquid water after simulation according to the index files, calculating and comparing nucleation barriers, and predicting the anti-freezing property of pectin. According to the method, pectin with different molecular structures is constructed and behaviors of pectin in ice crystal nucleation are evaluated, so that the application cost is greatly reduced, and experimental resources are saved.

Description

Technical Field

[0001] The present invention relates to the field of food. More specifically, the present invention relates to a method for determining the antifreeze properties of pectin based on molecular dynamics simulation. Background Art

[0002] Freezing is a widely used processing and storage method for food, medicine and functional materials. By regulating the antifreeze components in the raw materials, the size and shape of ice crystals in the frozen products can be effectively regulated, which is beneficial to inhibit recrystallization and regulate product quality.

[0003] Antifreeze polysaccharides are a type of polysaccharide that inhibits ice nucleation and increases supercooling, and can form small ice crystal structures in the product during the freezing process. Due to its large molecular weight, the antifreeze polysaccharide molecules can fully stretch in the raw material system and form a large number of hydrogen bonds with water molecules, which increases the nucleation energy of the system, inhibits nucleation, and thus increases the supercooling. Therefore, antifreeze polysaccharides have the ability to form small ice crystals in the raw materials after freezing.

[0004] The molecular weight of natural polysaccharides ranges from 5kDa to 5000kDa. They are widely found in plants and fungi and can be obtained through a variety of extraction processes. They have low production costs and stable performance, making them more cost-effective than antifreeze proteins from animal sources. Previous studies have found that many polysaccharides have the activity of inhibiting the reduction of nucleation temperature, but no thermal hysteresis activity. Therefore, it is difficult to determine whether polysaccharides have the antifreeze property of inhibiting ice nucleation. Previous studies usually judged the property of inhibiting ice crystal growth based on the size of the binding energy of antifreeze substances with water molecules during the growth of ice crystals, but could not predict the property of supercooling the reaction system. Pectin is a polysaccharide composed of HG, RGI and RGII. It is widely used in food as a thickener, stabilizer, emulsifier, etc., but previous studies have not paid attention to the effect of pectin on the freezing characteristics of products. A full understanding of the antifreeze activity of pectin in inhibiting ice crystal nucleation is conducive to expanding the application range of pectin and promoting the development of frozen foods. At present, no method for predicting the antifreeze properties of pectin has been reported so far. Summary of the invention

[0005] The purpose of the present invention is to provide a method for determining the antifreeze properties of pectin based on molecular dynamics simulation. Starting from the practicality of pectin, pectins with different molecular structures are constructed and their behaviors in ice crystal nucleation are evaluated, thereby greatly reducing application costs, saving experimental resources, and guiding the design and development of new antifreeze active polysaccharides, reducing the time from research to industrialization.

[0006] In order to achieve these objects and other advantages of the present invention, a method for determining the antifreeze properties of pectin based on molecular dynamics simulation is provided, comprising:

[0007] Step 1: Construction of nucleation model systems with different structures: first construct an ice layer and generate a basic skeleton of pectin, then construct two structure files: add ice layer and pectin molecules, retain a spherical structure with a certain distance centered on the pectin molecule with a degree of polymerization of D, and make the number of water molecules in the retained structure between 0.95N and 1.05N; make the pectin molecule with a degree of polymerization of D located in the center, add a water layer and sodium ions, retain the structure other than the spherical structure with a certain distance centered on the pectin molecule, and merge the two structures to obtain a nucleation model system, that is, a cluster embedded with ice seeds, and finally build a box for the constructed system;

[0008] The calculation formula of N is as follows:

[0009]

[0010] In the above formula, c is the pectin concentration under actual conditions, g / g; 194.139 is the molar mass of galacturonic acid constituting pectin, D is the degree of polymerization of simulated pectin, and 18 is the molar mass of water molecules;

[0011] Step 2: Use embedded ice seeds for nucleation simulation: Construct a force field file. To ensure the normal operation of the system constructed in step 1, first minimize the energy, then supercool, and control the pressure balance to make the molecules in each cluster model reach equilibrium. At this time, calculate the number of water molecules N0 that form ice in each cluster;

[0012] Step 3: Simulate and calculate the critical temperature: To clarify the critical temperature T at which the ice clusters neither grow nor melt in the system constructed in step 1 L , by performing 5-100 simulations at 200-268K for 1-10ns, during which the number of water molecules N in the hexagonal ice structure is calculated I The number of water molecules N with non-hexagonal ice structure II , when in the simulation process at a certain temperature, N I and N II Neither increasing nor decreasing, the temperature can be determined as T L ;

[0013] Step 4: Perform simulation for 10 to 20 ns at 1 bar and different supercooling temperatures T, wherein the supercooling temperature T is as low as 30 K below the critical temperature or the actual freezing temperature, identify and output the structure file according to the trajectory file after simulation, and establish the index file of the water molecules forming ice and the index file of the water molecules of liquid water in the file according to the last frame structure file, and calculate the free energy difference Δμ between the solid water and the liquid water after simulation according to the above index files;

[0014] Step 5: Calculate the nucleation barrier G. The calculation formula of the nucleation barrier G is as follows:

[0015]

[0016] Preferably, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in the step 1, an ice layer is constructed using Genice or Genice2, a basic skeleton and force field of pectin are generated using CHARMM-GUI online software, and the fine structure of pectin is modified using Pymol; then two structure files are constructed: ice layer and pectin molecules are added using Packmol, a spherical structure with a certain distance centered on pectin with a degree of polymerization of D is selected and retained using VMD, and the number of water molecules in the retained structure is between 0.95N and 1.05N; pectin molecules with a degree of polymerization of D are located in the center using Packmol, a water layer and sodium ions are added, structures other than the spherical structure with a certain distance centered on the pectin molecules are selected and retained using VMD, and the two structures are merged using Packmol to obtain a nucleation model system, and finally a box is established for the constructed system using Gromacs so that the water molecules are 0.2nm away from the edge of the box.

[0017] Preferably, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in the step 2, the boundary conditions of the box are set to periodic boundaries, the energy minimization process is simulated using Gromacs or NAMD software, so that the maximum force is <100 kJ / mol, the force field type is charmm36, charmm22 or OPLS force field, and the CHILL+ algorithm is used to calculate the number of water molecules N0 that form ice in the cluster.

[0018] Preferably, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in step three, the error is reduced to less than 2% through multiple simulations.

[0019] Preferably, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in step 4, simulation is performed by Gromacs, the CHILL+ algorithm is used to identify solid and liquid water molecules, and the structure file is output, and the free energy difference Δμ between the simulated solid water and liquid water is calculated by the energy command.

[0020] Preferably, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in the step 1, pectin molecules with different surface functional groups and different polymerization degrees are used to construct a pectin model, the surface functional groups include amino, alkyl, ferulic acid and ester groups, and the polymerization degree D is 4-12; water molecules are selected from the TIP4P / ice type.

[0021] Preferably, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in step 2, supercooling is performed at 180K, the pressure control method is selected as the C-rescale method, the pressure control balance is 100ps, and the pressure is 1bar. Preferably, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in step 3, the Chill+ algorithm is used to calculate the number of water molecules N in the hexagonal ice structure I The number of water molecules N with non-hexagonal ice structure II .

[0022] The present invention has at least the following beneficial effects:

[0023] The present invention proposes antifreeze pectin and develops a comprehensive antifreeze property research method based on the quantitative calculation, equilibrium temperature prediction and chemical potential prediction of the hexagonal ice-water molecular structure, which has a guiding role in the development of ice crystal structure regulating substances based on antifreeze polysaccharides.

[0024] The present invention starts from the practicality of pectin, constructs pectins with different molecular structures and evaluates their behaviors in ice crystal nucleation, thereby greatly reducing application costs, saving experimental resources, guiding the design and development of new antifreeze active polysaccharides, and shortening the time from research to industrialization.

[0025] Other advantages, objectives and features of the present invention will be embodied in part through the following description, and in part will be understood by those skilled in the art through study and practice of the present invention. BRIEF DESCRIPTION OF THE DRAWINGS

[0026] Figure 1 is a flowchart of a method for determining the antifreeze properties of pectin based on molecular dynamics simulation according to the present invention;

[0027] Figure 2 is a box diagram of a nucleation model system according to embodiment 1 of the present invention;

[0028] Figure 3 The implementation example 1 of the present invention adopts the CHILL+ algorithm to operate the page graph;

[0029] Figure 4 It is a box diagram of the nucleation model system of implementation 2 of the present invention. DETAILED DESCRIPTION

[0030] The present invention is further described in detail below in conjunction with the accompanying drawings so that those skilled in the art can implement the invention with reference to the description.

[0031] It should be noted that the experimental methods described in the following embodiments are conventional methods unless otherwise specified, and the reagents and materials can be obtained from commercial channels unless otherwise specified.

[0032] like Figure 1 As shown, the present invention provides a method for determining the antifreeze properties of pectin based on molecular dynamics simulation, comprising:

[0033] Step 1: Construction of nucleation model systems with different structures: first construct an ice layer and generate a basic skeleton of pectin, then construct two structure files: add ice layer and pectin molecules, retain a spherical structure with a certain distance (L) centered on the pectin molecule with a degree of polymerization of D, and make the number of water molecules in the retained structure between 0.95N and 1.05N; make the pectin molecule with a degree of polymerization of D located in the center, add a water layer and sodium ions, retain the structure other than the spherical structure with a certain distance (L) centered on the pectin molecule, and merge the two structures to obtain a nucleation model system, that is, a cluster embedded with ice seeds, and finally build a box for the constructed system;

[0034] The calculation formula of N is as follows:

[0035]

[0036] In the above formula, c is the pectin concentration under actual conditions, g / g; 194.139 is the molar mass of galacturonic acid constituting pectin, D is the degree of polymerization of simulated pectin, and 18 is the molar mass of water molecules;

[0037] Step 2: Use embedded ice seeds for nucleation simulation: Construct a force field file. To ensure the normal operation of the system constructed in step 1, first minimize the energy, then supercool, and control the pressure balance to make the molecules in each cluster model reach equilibrium. At this time, the CHILL+ algorithm is used to calculate the number of water molecules N0 that form ice in each cluster.

[0038] Step 3: Simulate and calculate the critical temperature: To clarify the critical temperature T at which the ice clusters neither grow nor melt in the system constructed in step 1 L , 5-100 simulations of 1-10 ns are performed at 200-268 K (the higher the temperature, the shorter the simulation time), where the temperature selection method is a binary search method, lowering the temperature when the ice nucleus melts, and raising the temperature when the ice nucleus grows, until a temperature is found where the cluster neither grows nor melts, during which the number of water molecules N in the hexagonal ice structure is calculated I The number of water molecules N with non-hexagonal ice structure II (The CHILL+ algorithm is used to calculate the number of water molecules forming ice and liquid water molecules in the cluster). During the simulation at a certain temperature, N I and N II Neither increasing nor decreasing, the temperature can be determined as T L ;

[0039] Step 4: Perform simulations for 10 to 20 ns at 1 bar and different supercooling temperatures T, where the supercooling temperature T is as low as 30 K below the critical temperature, and the supercooling temperature T is T L -5K, T L -10K, T L -15K, T L -20K, T L -25K, T L –30K. Due to the variable freezing environment of actual frozen materials, multiple supercooling temperatures can be selected, and can also be selected according to the actual freezing temperature. At the same time, according to actual conditions, the supercooling temperature difference is generally less than 30K, so the lowest to the critical temperature T L -30K. Identify and output the structure file according to the trajectory file after simulation, establish the index file of water molecules forming ice and the index file of water molecules in liquid water according to the last frame structure file, and calculate the free energy difference Δμ between solid water and liquid water after simulation according to the above index files;

[0040] Step 5: Calculate the nucleation barrier G. The calculation formula of the nucleation barrier G is as follows:

[0041]

[0042] In another embodiment, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in step 1, an ice layer is constructed using Genice or Genice2, a basic skeleton and force field of pectin are generated using CHARMM-GUI online software, and the fine structure of pectin is modified using Pymol; then two structure files are constructed: ice layer and pectin molecules are added using Packmol, a spherical structure with a certain distance centered on pectin with a degree of polymerization of D is selected and retained using VMD, and the number of water molecules in the retained structure is between 0.95N and 1.05N; pectin molecules with a degree of polymerization of D are located in the center using Packmol, a water layer and sodium ions are added, structures other than the spherical structure with a certain distance centered on the pectin molecules are selected and retained using VMD, and the two structures are merged using Packmol to obtain a nucleation model system, and finally a box is established for the constructed system using Gromacs so that the water molecules are 0.2nm away from the edge of the box.

[0043] In another embodiment, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in step 2, the boundary conditions of the box are set to periodic boundaries, the energy minimization process is simulated using Gromacs or NAMD software, so that the maximum force is <100 kJ / mol, the force field type is charmm36, charmm22 or OPLS force field, and the CHILL+ algorithm is used to calculate the number of water molecules N0 that form ice in the cluster.

[0044] In another embodiment, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in step three, the error is reduced to less than 2% through multiple simulations.

[0045] In another embodiment, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in step four, simulation is performed using Gromacs, the CHILL+ algorithm is used to identify solid and liquid water molecules, and the structure file is output, and the energy command is used to calculate the free energy difference Δμ between the simulated solid water and liquid water.

[0046] In another embodiment, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in step one, a pectin model is constructed using pectin molecules with different surface functional groups and different degrees of polymerization, the surface functional groups include amino, alkyl, ferulic acid and ester groups, and the degree of polymerization D is 4-12; water molecules are of TIP4P / ice type.

[0047] In another embodiment, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in step 2, supercooling is performed at 180K, the C-rescale method is selected for pressure control, the pressure control balance is 100ps, and the pressure is 1 bar.

[0048] In another embodiment, in the method for determining the antifreeze properties of pectin based on molecular dynamics simulation, in step 3, the Chill+ algorithm is used to calculate the number of water molecules N in the hexagonal ice structure. I The number of water molecules N with non-hexagonal ice structure II .

[0049] Example 1

[0050] The method for determining the antifreeze properties of pectin based on molecular dynamics simulation includes:

[0051] Step 1: Construction of nucleation model. To simulate a 2% pectin solution with a degree of esterification of 50%, an ice layer is first constructed to generate the basic skeleton of pectin, and then two structure files are constructed: adding ice layer and pectin molecules, retaining a spherical structure with a certain distance (3.4nm) centered on the pectin molecule with a degree of polymerization of D, and making the number of water molecules in the retained structure between 0.95N and 1.05N; making the pectin molecule with a degree of polymerization of D at the center, adding a water layer and sodium ions, retaining the structure other than the spherical structure with a certain distance (3.4nm) centered on the pectin molecule, and merging the two structures to obtain a nucleation model system, that is, a cluster embedded with ice seeds, and finally building a box for the constructed system;

[0052] The calculation formula of N is as follows:

[0053]

[0054] In the above formula, c is the pectin concentration under actual conditions, g / g; 194.139 is the molar mass of galacturonic acid constituting pectin, D is the degree of polymerization of simulated pectin, and 18 is the molar mass of water molecules;

[0055] Among them, Genice was used to construct the ice layer, CHARMM-GUI online software was used to generate the basic skeleton and force field of pectin, and Pymol was used to modify the fine structure of pectin; then two structure files were constructed: Packmol was used to add ice layer and pectin molecules, VMD was used to select and retain a spherical structure centered on pectin with a degree of polymerization of D, and the number of water molecules in the retained structure (integer) was made between 0.95N and 1.05N; Packmol was used to make the pectin molecule with a degree of polymerization of D located in the center, water layer and sodium ions were added, VMD was used to select and retain structures other than the spherical structure centered on the pectin molecule at a certain distance, and Packmol was used to merge the two structures to obtain a nucleation model system, and finally Gromacs was used to build a box for the constructed system so that the water molecules were 0.2nm away from the edge of the box.

[0056] Specific operation: The basic skeleton of pectin molecule with 12 polymerization degree (in this case, D is 12, simulating pectin with polymerization degree 12) and force field are generated by CHARMM-GUI online software. Pymol is used to modify the fine structure of pectin, and methyl groups are added at 6 carboxyl groups. The ice layer is modeled by Genice, and the water molecules are selected by TIP4P / ice type. Packmol is used to add ice layer and pectin molecules, so that the pectin molecules are located in the center of the ice layer, and VMD is used to select and retain a spherical structure with a certain distance (3.4nm) centered on the pectin, so that the number of water molecules in the retained structure is 6200; Packmol is then used to add water layer (20,000 water molecules), 6 sodium ions, and pectin molecules, and VMD is used to select and retain structures other than the spherical structure with a certain distance (3.4nm) centered on the pectin (the number of non-solid water molecules is 12,000), and finally Packmol is used to merge the two structures to obtain the nucleation model system. Gromacs is used to build a box for the established system, so that the water molecules are 0.2nm away from the edge of the box. The final model structure is as follows Figure 2 shown.

[0057] The calculation formula of N is as follows:

[0058]

[0059] Wherein: c is the pectin concentration under actual conditions, g / g; 194.139 is the molar mass of galacturonic acid constituting pectin; 12 is the degree of polymerization of simulated pectin; and 18 is the molar mass of water molecules.

[0060] Step 2: Equilibrium process: Use Gromacs to set the box boundary conditions to periodic boundaries. Construct the force field file and use the CHARMM36 all-atom force field. In order to make the system run normally, first use Gromacs to minimize the energy to F<100, then supercool at 180K, the pressure is 1 bar, the system pressure control selects the C-rescale method, and balances for 100ps to make the molecules in the cluster model reach equilibrium. At this time, the CHILL+ algorithm is used, and the operation page is as follows: Figure 3 As shown, the number of water molecules N0 that form ice in the cluster is calculated and used for the subsequent calculation of the nucleation barrier.

[0061] Step 3: To clarify the critical temperature at which the ice clusters in the system neither grow nor melt, Gromacs was used to perform 10 simulations of 5 ns at 200-268 K (the lower the temperature, the shorter the simulation time). The temperature selection method was a binary search method. When the ice nucleus melted, the temperature was lowered, and when the ice nucleus grew, the temperature was increased until the temperature at which the clusters neither grew nor melted was found. At the same time, the error was reduced to less than 2% through multiple simulations. During this period, the number of water molecules N in the hexagonal ice structure was calculated. I The number of water molecules N with non-hexagonal ice structure II (The CHILL+ algorithm is used to calculate the number of water molecules forming ice and liquid water molecules in the cluster). During the simulation at a certain temperature, N I and N II It neither increases nor decreases, that is, this temperature can be determined as the critical temperature (T L ). The final critical temperature is shown in Table 1.

[0062] Step 4: Further use Gromacs to simulate for 10ns at 1 bar and supercooling temperature T, where the supercooling temperature T is -40℃ based on the actual freezing temperature, and the simulated supercooling temperature T is 233K. Based on these simulated trajectory files, use the CHILL+ algorithm to identify solid and liquid water molecules, output structure files, establish the index of water molecules that form ice and the index of water molecules in liquid water, and use the energy command of Gromacs to calculate the free energy difference Δμ between solid water and liquid water after simulation.

[0063] Step 5: Calculate the nucleation barrier G:

[0064]

[0065] Example 2

[0066] The difference from Example 1 is that a 2% concentration pectin solution with a degree of amidation of 50% is simulated, and the fine structure of pectin is modified by Pymol, methyl groups are added to 3 carboxyl groups, and amino groups are added to 6 carboxyl groups. The rest is the same as Example 1. The final model structure is as follows Figure 4 shown.

[0067] The critical temperature, initial number of solid water molecules, and nucleation barrier obtained in Example 1 and Example 2 are shown in Table 1.

[0068] Table 1 Critical temperature, initial number of solid water molecules, and nucleation barrier

[0069]

[0070] Supercooling refers to the degree to which the temperature of a liquid is lower than its freezing point when it is not crystallized. The solution with a larger supercooling degree is more difficult to nucleate and more resistant to freezing. The relationship between supercooling and nucleation barrier is that an increase in nucleation barrier usually leads to an increase in supercooling. Therefore, the difficulty of nucleation can be predicted by comparing the size of nucleation barrier. That is, if you want to compare which pectin has a larger supercooling degree and is more resistant to freezing, you can use this method to predict which pectin has a larger nucleation barrier. Table 1 shows that under -40°C freezing conditions, the nucleation barrier of a 2% concentration pectin solution with an amidation degree of 50% is lower than that of a 2% concentration pectin solution with an esterification degree of 50%. In the actual test system, the supercooling temperature of a 2% concentration pectin solution with an esterification degree of 50% is -12°C (supercooling degree is 12°C), and the supercooling temperature of a 2% concentration pectin solution with an amidation degree of 50% is -10°C (supercooling degree is 10°C), indicating that pectin with an esterification degree of 50% has stronger frost resistance. The simulation method of the present application can compare and predict the freezing resistance of pectins with different structures.

[0071] Although the embodiments of the present invention have been disclosed as above, they are not limited to the applications listed in the specification and the implementation modes, and they can be fully applied to various fields suitable for the present invention. For those familiar with the art, additional modifications can be easily implemented. Therefore, without departing from the general concept defined by the claims and the scope of equivalents, the present invention is not limited to the specific details and the illustrations shown and described herein.

Claims

1. A method for determining the antifreeze properties of pectin based on molecular dynamics simulation, characterized in that: include: Step 1: Construction of nucleation model systems with different structures: first construct an ice layer and generate a basic skeleton of pectin, then construct two structure files: add ice layer and pectin molecules, retain a spherical structure with a certain distance centered on the pectin molecule with a degree of polymerization of D, and make the number of water molecules in the retained structure between 0.95N and 1.05N; make the pectin molecule with a degree of polymerization of D located in the center, add a water layer and sodium ions, retain the structure other than the spherical structure with a certain distance centered on the pectin molecule, and merge the two structures to obtain a nucleation model system, that is, a cluster embedded with ice seeds, and finally build a box for the constructed system; The calculation formula of N is as follows: In the above formula, c is the pectin concentration under actual conditions, g / g; 194.139 is the molar mass of galacturonic acid constituting pectin, D is the degree of polymerization of simulated pectin, and 18 is the molar mass of water molecules; Step 2: Use embedded ice seeds for nucleation simulation: Construct a force field file. To ensure the normal operation of the system constructed in step 1, first minimize the energy, then supercool, and control the pressure balance to make the molecules in each cluster model reach equilibrium. At this time, calculate the number of water molecules N0 that form ice in each cluster; Step 3: Simulate and calculate the critical temperature: To clarify the critical temperature T at which the ice clusters neither grow nor melt in the system constructed in step 1 L , by performing 5-100 simulations at 200-268K for 1-10ns, during which the number of water molecules N in the hexagonal ice structure is calculated I The number of water molecules N with non-hexagonal ice structure II , when in the simulation process at a certain temperature, N I and N II Neither increasing nor decreasing, the temperature can be determined as T L ; Step 4: Perform simulation for 10 to 20 ns at 1 bar and different supercooling temperatures T, wherein the supercooling temperature T is as low as 30 K below the critical temperature or the actual freezing temperature, identify and output the structure file according to the trajectory file after simulation, and establish the index file of the water molecules forming ice and the index file of the water molecules of liquid water in the file according to the last frame structure file, and calculate the free energy difference Δμ between the solid water and the liquid water after simulation according to the above index files; Step 5: Calculate the nucleation barrier G. The calculation formula of the nucleation barrier G is as follows:

2. The method for determining the antifreeze properties of pectin based on molecular dynamics simulation according to claim 1, characterized in that: In the step 1, an ice layer is constructed using Genice or Genice2, a basic skeleton and force field of pectin are generated using CHARMM-GUI online software, and the fine structure of pectin is modified using Pymol; then two structure files are constructed: ice layer and pectin molecules are added using Packmol, a spherical structure with a certain distance centered on pectin with a degree of polymerization of D is selected and retained using VMD, and the number of water molecules in the retained structure is between 0.95N and 1.05N; pectin molecules with a degree of polymerization of D are located at the center using Packmol, a water layer and sodium ions are added, structures other than the spherical structure with a certain distance centered on the pectin molecules are selected and retained using VMD, and two structures are merged using Packmol to obtain a nucleation model system, and finally a box is established for the constructed system using Gromacs so that the water molecules are 0.2nm away from the edge of the box.

3. The method for determining the antifreeze properties of pectin based on molecular dynamics simulation as claimed in claim 1, characterized in that: In the step 2, the box boundary condition is set to a periodic boundary, the energy minimization process is simulated using Gromacs or NAMD software, and the maximum force is <100 kJ / mol. The force field type is charmm36, charmm22 or OPLS force field, and the CHILL+ algorithm is used to calculate the number of water molecules N0 that form ice in the cluster.

4. The method for determining the antifreeze properties of pectin based on molecular dynamics simulation as claimed in claim 1, characterized in that: In the step three, the error is reduced to below 2% through multiple simulations.

5. The method for determining the antifreeze properties of pectin based on molecular dynamics simulation as claimed in claim 1, characterized in that: In the step 4, simulation is performed by Gromacs, solid and liquid water molecules are identified by CHILL+ algorithm, and structure files are output, and the free energy difference Δμ between the simulated solid water and liquid water is calculated by energy command.

6. The method for determining the antifreeze properties of pectin based on molecular dynamics simulation as claimed in claim 1, characterized in that: In the step 1, pectin molecules with different surface functional groups and different polymerization degrees are used to construct a pectin model, wherein the surface functional groups include amino, alkyl, ferulic acid and ester groups, and the polymerization degree D is 4-12; and the water molecules are of TIP4P / ice type.

7. The method for determining the antifreeze properties of pectin based on molecular dynamics simulation as claimed in claim 1, characterized in that: In the step 2, supercooling is performed at 180 K, the C-rescale method is selected for pressure control, the pressure control balance is 100 ps, ​​and the pressure is 1 bar.

8. The method for determining the antifreeze properties of pectin based on molecular dynamics simulation as claimed in claim 1, characterized in that: In step 3, the Chill+ algorithm is used to calculate the number of water molecules N in the hexagonal ice structure. I The number of water molecules N with non-hexagonal ice structure II .

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