Abstract
Coarse-grained (CG) water models with explicit electrostatic interactions are essential for capturing the dielectric response of biomolecular systems. However, many CG water models exhibit pronounced freezing artifacts under ambient conditions. Using the SPICA force-field family as a case study, we examined the influences of charge topology, background dielectric screening (εbg), and Lennard–Jones (LJ) interaction strength on the freezing tendency of CG water. Among the models examined here, which all reproduce the target density and surface tension at 298 K, changing the charge topology from a linear dipole to V-shaped geometries did not substantially lower the melting temperature (T m). Instead, T m was more sensitive to the LJ interaction strength. Reducing εbg strengthens the electrostatic contribution, allowing the LJ attraction to be weakened while maintaining the target properties. On this basis, we propose a parametrization framework for introducing a permanent dipole into a nonpolar CG water model while mitigating its freezing tendency. Using this framework, we developed pSPICA2, which reduces T m from 384 to 302 K while retaining accurate density, surface tension, and dielectric response at 298 K. Although T m remains above the experimental value of 273 K in this work, the proposed framework offers a practical route for developing polar CG water models with reduced freezing artifacts.


Introduction
Molecular dynamics (MD) simulations have become an important tool for investigating the structural, dynamical, and thermodynamic behavior of biological systems and soft-matter assemblies. Despite substantial advances in computer hardware and simulation algorithms, all-atom (AA) MD simulations remain fundamentally constrained in the time and length scales that they can access. This limitation restricts their applicability to many biologically relevant processes that occur on microsecond or longer time scales or involve mesoscale structural reorganization. Coarse-grained (CG) force fields (FFs) address this limitation by reducing the number of degrees of freedom, thereby extending accessible simulation time and length scales while retaining essential physicochemical features of the underlying molecular interactions. −
Among the CG FFs developed for biomolecular simulations, the MARTINI FF has become one of the most widely used frameworks because of its systematic parametrization based on partitioning free energies and its broad applicability to lipids, proteins, and other biomolecules. ,− Its applications now extend well beyond lipid membranes to proteins, carbohydrates, and intrinsically disordered proteins, reflecting the continuing refinement and growing versatility of the framework. ,, Independently, the SPICA FF (formerly the SDK FF) emphasizes the reproduction of experimental interfacial tensions and densities, together with distribution functions derived from AA-MD reference simulations. − The SPICA FF has demonstrated strong performance in describing domain formation and the mesoscale morphology of lipid assemblies. ,,
Because water mediates nearly all intermolecular interactions relevant to the structures and dynamics in biological assemblies, the fidelity of the water representation directly constrains the range of phenomena a CG FF can capture. − Accordingly, CG water models have been developed with different target properties for different CG FF frameworks. In their standard forms, both MARTINI and SPICA represent water as a single uncharged particle and use an implicit background dielectric constant to approximate electrostatic screening. , The two frameworks, however, prioritize distinct target properties. The MARTINI water model is parametrized primarily to reproduce partitioning free energies between polar and apolar phases across a broad set of compounds, supporting transferability among lipids, proteins, and other biomolecules. , By contrast, the SPICA water model is parametrized to reproduce experimental water density, surface and interfacial tension, together with solvation or transfer free energies of various solutes derived from AA-MD reference data, which are important for characterizing self-assembled surfactant and lipid structures. Recent comparative studies have also reported that the SPICA water model reproduces the experimental enthalpy of vaporization, isothermal compressibility, and self-diffusion coefficient more accurately than other widely used nonpolar CG water models.
Although computationally efficient, uncharged water models with implicit dielectric screening cannot explicitly represent the local dielectric response of water. This limitation becomes important in processes involving strong local electric fields or charge-driven structural transitions, such as membrane electroporation. , To address this issue, several CG water models incorporate explicit electrostatic interactions through permanent charge distributions or polarizable representations. These models typically distribute partial charges onto additional off-center sites that carry no van der Waals interaction, a design analogous to the charge-only M site of the TIP4P water model and to the dummy sites in cationic dummy-atom models of metal ions. , Permanent-charge models embed fixed point charges within each CG water particle to generate an electric dipole and, in some cases, higher-order multipoles, thereby enabling an explicit response to the local electrostatic environment. ,,− The big multipole water (BMW) model uses three charged sites to reproduce both the dipole and quadrupole moment tensor of water clusters. , The polar pSPICA water model employs a simpler two-site dipolar representation optimized within the SPICA parametrization framework. , In contrast, the polarizable MARTINI water model contains a dipole that responds dynamically to the local electric field rather than remaining fixed. These charge-bearing models have been used to simulate membrane electroporation and ion transport across lipid bilayers, illustrating the importance of explicit electrostatic degrees of freedom in CG water representations. ,,,
A separate and persistent challenge in CG water modeling is the occurrence of freezing artifacts. Systematic parameter-space scans have shown that the freezing tendency is an intrinsic limitation of many uncharged CG water models: the melting temperature (T m) generally increases with the level of coarse-graining and as the nonbonded potential becomes steeper or shorter-ranged. , Both the SPICA and pSPICA water models use relatively strong van der Waals (vdW) interactions to reproduce the high surface tension of water and, as shown below, exhibit substantial freezing artifacts. To mitigate this problem, the standard MARTINI water model includes a small fraction of antifreeze particles with a slightly larger vdW radius. These particles disrupt local crystalline packing while preserving the parametrized bulk thermodynamic properties. The more recent Martini3 FF represents bulk water as a mixture of CG sites of three different sizes to address this persistent artifact. , Maintaining a uniform mixture composition from the bulk to interfaces, however, remains challenging.
By contrast, a comparable freezing artifact has not been reported for the BMW model, which uses a three-site dipole–quadrupole representation. ,, This behavior may be related to the softer repulsive core of the Born-Mayer-Huggins potential used in that model. However, the BMW model was parametrized and validated at only one ambient temperature, which limits assessment of its performance over a wider temperature range.
The SPICA water model provides a useful basis for examining this issue because it reproduces several liquid-water properties, including density, surface and interfacial tensions, and solvation free energies, more accurately than several commonly used nonpolar CG water models. , In addition, pSPICA introduces a two-site permanent dipole while retaining the accuracy of selected bulk-water properties. Together, these models provide a framework for examining how charge representation and nonbonded interaction parameters are associated with the freezing artifact. We considered three charge topologiesuncharged, two-site dipolar, and three-site multipolarwithin the SPICA/pSPICA framework, and evaluated their melting behavior and freezing kinetics. Because each model was parametrized to reproduce the experimental density and surface tension, the charge topology and nonbonded parameters cannot be varied independently. The comparison therefore addresses how different charge representations, as a design degree of freedom under realistic parametrization constraints, affect the freezing behavior of CG water.
Permanent-charge CG water models commonly use a background dielectric constant, εbg, to complement the explicit charge representation. ,, However, the influence of εbg on the balance between electrostatic and vdW interactions has not been systematically examined in the context of freezing suppression. We therefore explored εbg as a design parameter and asked whether strengthening the explicit electrostatic contribution could permit a reduction in the LJ attraction while preserving selected target properties of liquid water. Our objective was to establish a parametrization strategy that mitigates the freezing artifact by rebalancing electrostatic and vdW interactions. Following this strategy, we developed pSPICA2, a new polar CG water model that has a substantially reduced T m and retains the dielectric response and thermodynamic accuracy within the SPICA/pSPICA framework.
Methods
CG Water Models with Different Charge Topologies
In the SPICA FF, three water molecules are mapped onto a single uncharged bead, denoted W. The W beads interact through a pairwise LJ potential. To compensate for the absence of an explicit molecular dipole, a high background dielectric constant of εbg = 80 is applied uniformly, corresponding to the assumption that electrostatic interactions between hydrated polar solutes are strongly screened. SPICA therefore serves here as a nonpolar reference for assessing models with explicit charge distributions. , The charge topologies of all models examined in this study are illustrated in Figure .
1.

Schematic representations of the CG water models investigated in this work. SPICA employs a single uncharged bead (W). pSPICA and the newly proposed pSPICA2 utilize a linear two-site topology with a bond length (r 0). p3SPICA-120 and p3SPICA-104.5 use three-site topologies with the same bond length (r 0) and bond angles (θ0) of 120° and 104.5°, respectively. The opaque sphere in SPICA and the transparent spheres in the polar models represent the vdW radii of the W and central WO sites, respectively. The small red and white spheres in the polar models indicate the positions of the WO and WH charge sites, respectively. Force-field parameters for all models are listed in Table . The figure was generated using VMD.
The pSPICA model introduces an explicit molecular dipole through a two-site representation while retaining the mapping ratio of three water molecules per CG particle. Each particle consists of a central WO bead and a satellite WH bead connected by a rigid bond of length r 0, with partial charges of −0.836e and +0.836e assigned to WO and WH, respectively. The LJ interaction is only assigned to the WO–WO pairs, whereas electrostatic interactions are evaluated between all intermolecular site pairs; the intraparticle WO–WH pair is excluded. The bond length and partial charges were chosen to yield a dipole moment of 4.4 D, corresponding to the average dipole moment of a three-water-molecule cluster obtained from AA-MD simulations.
With the introduction of the explicit dipole, εbg is reduced from 80 in SPICA to 3.2 in pSPICA. The LJ parameters were optimized to reproduce the experimental bulk density and air–water surface tension under ambient conditions, consistent with the SPICA parametrization strategy. ,, As described below, we also developed pSPICA2, which uses the same two-site topology but rebalances the vdW and electrostatic interactions to mitigate the freezing artifact observed in pSPICA.
To examine charge representation beyond a linear dipole, we constructed three-site CG water models in which two WH beads are bonded symmetrically to a central WO bead with bond length r 0 and an interbead angle θ0, forming a rigid V-shaped geometry analogous to that of an atomistic water molecule (Figure ). This topology, which is also used in the BMW model, ,, introduces a quadrupolar component that is absent from the two-site linear model while maintaining a net dipole moment of 4.4 D. We examined θ0 values of 120°, following the BMW model geometry, and 104.5°, corresponding to the experimental HOH bond angle of water. These models are denoted p3SPICA-120 and p3SPICA-104.5, respectively.
Force Field Parameters and Simulation Details
In the SPICA and pSPICA FFs, the nonbonded vdW interactions between CG water beads are described by Lennard–Jones potentials of the LJ 12–4, LJ 12–5 or LJ 9–6 form. These potentials can be written in the generic LJ m–n form
| 1 |
where σLJ denotes the vdW diameter parameter defined by U LJ(σLJ) = 0, ϵLJ determines the strength of the vdW interaction, and is the prefactor chosen to ensure the minimum of the LJ potential at σmin = (m/n)1/(m−n)σLJ equals −ϵLJ.
For SPICA water, the LJ 12–4 form (m = 12, n = 4) was selected for the W–W interaction because its steep repulsive term provided the best reproduction of liquid compressibility while simultaneously matching the experimental bulk density and surface tension under ambient conditions. , Nonwater vdW interactions in the SPICA FF employ the LJ 9–6 form (m = 9, n = 6). In pSPICA, the interaction between two central WO sites is described by the LJ 12–5 form (m = 12, n = 5). The p3SPICA-120 and p3SPICA-104.5 models also use the LJ 12–5 form for the WO–WO interaction. Following the original pSPICA parametrization, ϵLJ and σLJ were calibrated to reproduce the experimental density and surface tension of water at 298 K. In all models, LJ interactions were truncated at r cut = 15 Å. The complete LJ parameter sets are listed in Table .
1. Force Field Parameters for the CG Water Models Investigated in This Work.
| Model | εbg | LJ type m–n | ϵLJ (kcal/mol) | σLJ (Å) | Q WO (e) | Q WH (e) | r 0 (Å) | θ0 |
|---|---|---|---|---|---|---|---|---|
| SPICA | 80 | 12–4 | 0.895 | 4.371 | – | – | – | – |
| pSPICA | 3.2 | 12–5 | 1.050 | 4.400 | –0.836 | 0.836 | 1.100 | – |
| p3SPICA-120 | 3.2 | 12–5 | 0.952 | 4.430 | –1.248 | 0.624 | 1.474 | 120(°) |
| p3SPICA-104.5 | 3.2 | 12–5 | 0.994 | 4.410 | –0.942 | 0.471 | 1.595 | 104.5(°) |
| pSPICA2 | 1.5 | 12–4 | 0.698 | 4.485 | –0.541 | 0.541 | 1.700 | – |
Electrostatic interactions between all intermolecular charged-site pairs were calculated using the Coulomb potential
| 2 |
where Q i and Q j are the partial charges on sites i and j, ε0 is the permittivity of vacuum, and εbg is the background dielectric constant. In the nonpolar SPICA model, εbg = 80 is used to compensate for the absence of explicit charge sites and to represent strong electrostatic screening in a hydrated environment. In pSPICA, εbg = 3.2 is used to represent residual screening. The p3SPICA-120 and p3SPICA-104.5 models use the same value, εbg = 3.2, so that comparisons among the polar models are not additionally complicated by differences in the background dielectric constant. Short-range electrostatic interactions were calculated within the LJ cutoff of 15 Å, while long-range electrostatic interactions were evaluated using the particle–particle particle–mesh (PPPM) method. All intraparticle electrostatic interactions were excluded from the electrostatic calculation.
The purpose of incorporating a fixed dipole into each pSPICA water particle is to provide an explicit response to the local electrostatic environment. The original pSPICA parametrization yielded a relative dielectric permittivity, εr, of 80.7, calculated from equilibrium fluctuations of the total dipole moment using the Kirkwood–Froehlich relation
| 3 |
where M denotes the total dipole moment of the system, k B is the Boltzmann constant, and V and T are the system volume and temperature, respectively.
The BMW model instead used a PMF-based approach and reported an effective screening constant of εeff = 74. The use of a PMF-based measure was motivated by the explicit background dielectric constant, εbg = 1.3, in the BMW model. Because pSPICA similarly combines explicit dipoles with εbg = 3.2, the physical interpretation of the fluctuation-derived εr should be verified rather than assumed. We therefore treat εr from eq as an operational measure of the bulk dielectric response under the chosen Hamiltonian and compare it with an independently estimated εeff.
A direct PMF fit is less straightforward for SPICA water because the steep short-range repulsion produces pronounced solvent layering and corresponding oscillations in the PMF. To reduce the influence of these spatial oscillations, we measured the mean force between two test particles held at a fixed separation r while varying the magnitude Q of their charges. At a sufficiently large fixed separation, the mean force was fitted to
| 4 |
where ⟨⟩ denotes the ensemble average, and the constant C represents the charge-independent contribution from solvent structure at the selected separation. The separation was set to 32 Å, close to half the simulation-box length. This procedure assumes that the solvent-structure contribution is approximately independent of Q over the fitted charge range. The resulting εeff therefore represents the effective screening constant under the employed periodic boundary conditions. In addition, because the surrounding solvent may still reorganize in response to large test charges, εeff was used as an independent, qualitative cross-check of the fluctuation-derived εr rather than as a higher-precision dielectric estimate.
When the background dielectric constant εbg = 1, the mean-force-derived εeff should equal the fluctuation-derived εr. To test such consistency, we performed an additional simulation in which all pSPICA partial charges were scaled by with εbg = 3.2 while the background dielectric constant was reset to 1.0. The electrostatic force is then formally unchanged because
| 5 |
where is the scaled charge and εbg = 1 for the rescaled simulation. For this rescaled system, the dielectric permittivity εr obtained from dipole fluctuations can be compared directly with the effective screening constant εeff obtained from the force-fitting method. This comparison tests whether the two operational measures are mutually consistent. The comparison was then extended to the pSPICA system with εbg = 3.2 to cross-check the resulting εeff and εr values.
The intramolecular geometry of each polar CG water model was maintained using the SHAKE algorithm. For the two-site pSPICA model, the WO–WH bond length r 0 was constrained. For p3SPICA-120 and p3SPICA-104.5, the two WO–WH bond lengths and the WH–WO–WH angle θ0 were constrained simultaneously to maintain a rigid V-shaped geometry. As described below, the partial charges and bond length were adjusted jointly to reproduce a target static relative dielectric permittivity of approximately 80 while maintaining a net dipole moment of 4.4 D, as in pSPICA. The force-field parameters of pSPICA2 were determined using the reparameterization procedure described in the Results and Discussion section. The resulting parameter sets for all models are summarized in Table .
All CG-MD simulations were performed with LAMMPS. , Bulk-water systems contained 4800 CG water particles in cubic simulation cells with periodic boundary conditions in all three dimensions. Temperature was controlled using a Nosé–Hoover thermostat with a relaxation time of 1 ps, and pressure was controlled using a Parrinello–Rahman barostat with a relaxation time of 10 ps. − The equations of motion were integrated using the velocity-Verlet algorithm with a time step of 10 fs. Bulk-water simulations were conducted in the NPT ensemble at 1 atm over the temperature range of 290–363 K to obtain the density thermogram ρ(T).
Surface tension was calculated using a water-slab geometry. Starting from an equilibrated bulk configuration, the simulation box was extended to 150 Å along the z direction, creating two vacuum–water interfaces normal to the z axis. These simulations were conducted in the NVT ensemble. The surface tension, γ, was calculated from the diagonal components of the pressure tensor as
| 6 |
where L z is the box length in the z direction and P xx , P yy , and P zz are the diagonal components of the pressure tensor. The factor of 1/2 accounts for the two equivalent interfaces present in the slab system.
Characterization of the Operational Melting Temperature and Nucleation Dynamics
The melting behavior of each CG water model was characterized using a direct solid–liquid coexistence protocol. Two simulation cells containing 1200 CG water particles each were prepared: one was crystallized at low temperature to obtain a fully solid configuration, and the other contained liquid water equilibrated at 298 K and 1 atm. The cells were joined along the z direction to produce a 2400-particle system with the solid–liquid interface normal to z. Before the coexistence simulation, the combined system was energy-minimized and equilibrated for 10 ps to relax the interface. Production simulations were then performed in the NPT ensemble at 1 atm using an anisotropic barostat that allowed the three box dimensions to fluctuate independently, thereby permitting the solid phase to adopt its equilibrium lattice dimensions and minimizing artificial strain on the solid that could bias the measured T m.
Starting from the combined solid–liquid configuration, independent equilibrium simulations were performed at a series of temperatures in 1 K increments. In this work, T m was then defined as the lowest tested temperature at which the solid phase melted completely within the simulation time window. Because this criterion depends on the system size, the simulation time window, and the initial interface, the resulting T m should be interpreted as the operational T m rather than the exact equilibrium melting temperature. All models were nevertheless evaluated with an identical protocol, so the relative T m values remain a valid basis for comparing freezing tendency.
To characterize the propensity of each water model to freeze, nucleation simulations were performed at 240 K, a temperature sufficiently below the operational T m values of the original models to produce spontaneous crystallization within accessible simulation times. Each simulation was initialized from a liquid configuration of 1200 CG water particles pre-equilibrated at 298 K and 1 atm. Fifty starting configurations were extracted from a 10 ns pre-equilibration trajectory. Each configuration was quenched to 240 K and simulated at 1 atm using an anisotropic barostat, with the thermostat and barostat settings described above.
The growth of crystalline nuclei was monitored using a bond-orientational order parameter to classify CG water particles as solid-like or liquid-like. , For each particle i, the complex order-parameter vector q̅ 6m (i) was calculated using the freud package, , as
| 7 |
where Y 6m denotes a spherical harmonic of degree l = 6 and r̂ ij is the unit vector from particle i to particle j. The sum extends over the N b (i) neighbors within 6.0 Å, corresponding to the first minimum of the radial distribution function between CG water particles. Particles i and j were defined as having a crystalline connection when the normalized dot product of their order-parameter vectors satisfies
| 8 |
A particle was then classified as solid-like when it formed at least seven crystalline connections with its neighbors. , The largest contiguous cluster of solid-like particles in each frame was identified as the nucleus, and its size n was used as the nucleation order parameter.
From the 50 independent freezing trajectories, we calculated the mean first-passage time (MFPT), τ(n), defined as the average time required for the largest crystalline nucleus to reach size n for the first time. , To obtain comparative nucleation parameters, τ(n) was fitted to the sigmoidal function with the crystal-growth correction proposed by Yuhara et al.
| 9 |
where τ n is the critical nucleation time, n* is the fitted critical nucleus size, Z is the Zeldovich factor, R G is the postcritical crystal-growth rate, and C = 5 is a smoothing constant that activates the growth-correction term in the postnucleation regime. The nucleation free energy barrier was then estimated from the fitted parameters as ΔG*/k B T = 3π(n*)2 Z 2, following the classical-nucleation-theory-based treatment of Yuhara et al. All models were simulated under an identical protocol. The fitted ΔG* and R G therefore provide a consistent basis for comparing freezing behavior among the models, although their absolute values should not be interpreted as macroscopic nucleation parameters.
Results and Discussion
Comparison of CG Water Models with Different Charge Topologies
We first compared the bulk thermodynamic properties and effective dielectric screening of SPICA, pSPICA, p3SPICA-120, and p3SPICA-104.5. The parameters listed in Table were selected to reproduce the experimental density and surface tension at 298 K. Figure shows the temperature dependence of the bulk density, ρ(T), and air–water surface tension, γ(T), for these models, together with the corresponding experimental values over 290–363 K.
2.

Temperature dependence of (a) density and (b) surface tension of the CG water models SPICA, pSPICA, p3SPICA-120, and p3SPICA-104.5. The newly parametrized two-site polar CG water model, pSPICA2, is also included for comparison. Experimental values (Expt.) are shown for ref .
All four models reproduce the monotonic decrease in water density with increasing temperature, in qualitative agreement with experiment. Near 298 K, the calculated densities are within approximately 1% of the experimental value (∼0.997 g/cm3), indicating that all parameter sets reproduce the ambient density accurately. The ρ(T) profiles are also broadly similar among the models. All models show the same principal deviation from experiment: a systematic positive offset at lower temperatures and an underestimation at higher temperatures, with the two three-site models showing the greater high-temperature deviations. Because all models were parametrized with different nonbonded parameters to reproduce the density at 298 K, the observed deviations emerge outside the target state point. Such deviation may arise from the charge topology and its associated orientational correlations, the fitted nonbonded parameters, or their combined effects.
The surface-tension results show a similarly modest dependence on charge representation. The experimental slope dγ/dT is preserved reasonably well across all charge representations over the examined temperature range, in contrast to the model-dependent divergence seen in ρ(T) at elevated temperatures. The main difference is an upward offset of approximately 2–3 mN/m for pSPICA relative to the experiment and to the other models. This offset is more plausibly attributed to the specific parametrization than to the two-site topology itself.
We next evaluated the dielectric response of pSPICA by comparing the effective screening constant, εeff, obtained from the mean-force method (eq ) with the relative dielectric permittivity, εr, obtained from dipole fluctuations (eq ). Calculations were performed both for the standard pSPICA model with εbg = 3.2 and for the charge-scaled system with εbg = 1.0 as shown in Figure . For the charge-scaled system, the fitting of the mean force yielded εeff = 27.79, in good agreement with εr = 26.57 from the fluctuation method (eq ). For standard pSPICA, the corresponding values were εeff = 85.27 and εr = 80.7. Within the statistical precision of force measurements and the limitations of the finite periodic test system, this agreement supports the use of the fluctuation-derived εr as an operational measure of dielectric screening in pSPICA.
3.

Mean force between two test charges as a function of the charge magnitude (Q) at a fixed separation of (r = 32) Å for pSPICA with the default (εbg = 3.2) (black circles) and for the scaled-charges pSPICA system with (εbg = 1.0) (red squares). Error bars represent standard errors of the mean force estimated by bootstrapping. Solid lines represent fits to eq used to determine the effective screening constants (εeff).
Both ratios εeff/εeff ≈ 3.07 and εr/εr ≈ 3.04 are close to εbg = 3.2. This numerical agreement is consistent with the expected scaling of the direct Coulomb term for the two specifically compared Hamiltonians and with the independent analysis of Chiacchiera et al. However, whether this linear scaling extends beyond the two parameter sets examined here requires further validation, since changing εbg also alters the solvent structure and collective orientational correlations.
The mean-force data in Figure remained substantially scattered even after 50 ns of sampling for each test-charge magnitude, demonstrating the slow convergence of force-based estimates. These fluctuations limit the precision of the fitted εeff. We therefore used the mean-force analysis primarily to cross-check the fluctuation method and used eq for subsequent dielectric-permittivity calculations because it converged more readily under the present conditions.
In the two-site pSPICA model, Q WO = −0.836e, Q WH = +0.836e, and r 0 = 1.1 Å give a fixed dipole moment of 4.4 D, corresponding to the average dipole moment of a three-water-molecule cluster in the AA-MD reference simulations. The p3SPICA-120 and p3SPICA-104.5 models were likewise constrained to a net dipole moment of 4.4 D. At fixed net dipole moment, the calculated dielectric permittivity nevertheless depends on r 0. As shown in Figure , increasing r 0 from 1.0 to 1.5 Å decreased εr from 89 to 61, whereas the density and surface tension changed only slightly over the same range.
4.

Bulk density (black circles), surface tension (red squares), and relative dielectric permittivity (blue diamonds) of the pSPICA model as functions of the bond length (r 0), varied from 1.0 Å to 1.5 Å. The magnitudes of the partial charges (Q) were adjusted inversely with (r 0) to maintain a fixed dipole moment of 4.4 D.
This result shows that r 0 provides a useful parameter for tuning collective dipole fluctuations with comparatively little effect on the fitted mechanical properties over the range examined. Varying r 0 at a fixed net dipole moment alters the spatial charge distribution, molecular geometry, and orientational correlations. Any of these may contribute to the variation in system dipole fluctuation and hence the static dielectric permittivity.
Table summarizes the bulk-water properties of the four models at 298 K. The calculated density, surface tension, and relative dielectric permittivity agree closely with the corresponding experimental values for all parameter sets, with deviations within approximately 1% for ρ and 3% for γ and εr. Thus, the selected two- and three-site parametrizations reproduce the targeted ambient liquid properties to comparable accuracy. The agreement at 298 K therefore shows that the nonbonded parameters can be refitted for different charge representations to reproduce the target liquid properties.
2. Bulk-Water Properties and Ice-Nucleation Parameters of the CG Water Models .
| ρ (g/cm3) | γ (mN/m) | εr | T m (K) | ΔG* (kcal/mol) | n* | τn (ps) | R G (1/ps) | |
|---|---|---|---|---|---|---|---|---|
| Expt. | 0.997 | 72.0 | 78.4 | 273 | ||||
| SPICA | 1.000 | 72.0 | 339 | 1.70 | 23.3 | 249.1 | 3.56 | |
| pSPICA | 1.002 | 73.6 | 80.7 | 384 | 0.96 | 15.9 | 66.8 | 3.16 |
| p3SPICA-120 | 0.998 | 72.5 | 80.0 | 360 | 1.50 | 17.2 | 150.1 | 1.93 |
| p3SPICA-104.5 | 1.001 | 72.4 | 78.4 | 378 | 1.16 | 17.2 | 106.6 | 2.50 |
| pSPICA2 | 1.003 | 71.9 | 79.1 | 302 | - | - | - | - |
Bulk density (ρ), surface tension (γ), and relative dielectric permittivity (εr) were evaluated at 298 K, whereas the melting temperature (T m) was determined using the solid-liquid coexistence protocol. Experimental values are included for comparison. Ice-nucleation parameters, including the nucleation free-energy barrier (ΔG*), critical nucleus size (n*), critical nucleation time (τ n), and crystal growth rate (R G), were obtained from simulations at 240 K. For pSPICA2, freezing was observed in only one of 50 independent simulations at 240 K using the same protocol as for the other models. Consequently, the nucleation parameters for pSPICA2 were not evaluated.
Effects of Charge Representation on the Freezing Artifact of CG Water
Despite their similar ambient liquid properties, the four models exhibit markedly different operational T m as listed in Table . All values exceed the experimental melting temperature of 273 K, confirming a pronounced freezing tendency within the SPICA-family models under the present coexistence protocol. SPICA has the lowest operational T m, 339 K, whereas pSPICA has the highest, 384 K. The p3SPICA-120 and p3SPICA-104.5 values are intermediate at 360 and 378 K, respectively. The polar models therefore have higher operational melting temperatures than nonpolar SPICA among the parameter sets examined.
Because the models differ not only in charge topology but also in LJ functional form and fitted LJ parameters under the parametrization constraints of density and surface tension, the higher T m of the polar models cannot be attributed uniquely to the charge topology. Redistributing the charges over a V-shaped geometry lowers T m relative to two-site pSPICA, substantially for p3SPICA-120 and only modestly for p3SPICA-104.5. Yet T m of both three-site models remain well above that of nonpolar SPICA. The key factor governing T m is examined in the following section.
To further compare freezing behavior, we calculated the mean first-passage time (MFPT) τ as a function of the largest crystalline nucleus size at 240 K from 50 independent trajectories. Figure shows sigmoidal MFPT profiles for all four models, with an initial increase followed by a plateau after the nucleus passes the fitted critical size n*. The magnitude and shape of the curves differ substantially, indicating distinct nucleation and growth dynamics under the common quench protocol.
5.

Mean first-passage time (MFPT), τ, as a function of the size of the largest nucleus, n, for SPICA, pSPICA, p3SPICA-120, and p3SPICA-104.5 at 240 K. The size of the largest nucleus is defined as the number of W or WO beads comprising the largest crystalline cluster, as described in the Methods section. Solid lines represent the simulation data, while dashed lines show fits of the MFPT data to eq . The nucleation free energy barrier (ΔG*), critical nucleus size (n*), critical nucleation time (τn), and crystal growth rate (R G) extracted from the fits are summarized in Table .
The MFPT-derived parameters in Table broadly follow the ordering of the operational melting temperatures. pSPICA has the smallest fitted ΔG*, n*, and τn, whereas SPICA has the largest values. At the common quench temperature of 240 K, a model with a higher T m experiences greater supercooling relative to its own melting point and therefore generally has a larger thermodynamic driving force for crystallization. The difference provides a straightforward explanation for at least part of the ordering in ΔG*, n*, and τn. Charge representation and the fitted nonbonded interactions may also influence the solid–liquid interfacial free energy and local ordering pathways. Separating these contributions would require calculations beyond the present comparative MFPT analysis.
The postcritical growth rate R G shows a different ordering: SPICA > pSPICA > p3SPICA-104.5 > p3SPICA-120, with SPICA giving R G = 3.56 ps–1 and the three-site models giving the lowest values. This trend is consistent with an orientational contribution to particle attachment. The isotropic nonpolar SPICA particles can attach to a growing crystalline cluster without first satisfying an explicit charge orientation. A fixed linear dipole introduces an orientational constraint, whereas a rigid V-shaped charge distribution introduces additional geometric specificity. These factors may slow postcritical growth in the polar models. The lower R G of p3SPICA-120 relative to p3SPICA-104.5 is also consistent with a greater orientational or packing penalty for the more open geometry, although the present data do not resolve this finer distinction.
Taken together, the coexistence and MFPT results show that models with similar ambient density, surface tension, and dielectric response can nevertheless have very different freezing behavior. The ordering of T m does not follow the charge topology, whereas R G decreases systematically from the isotropic model to the linear dipole and then to the two V-shaped models. Charge topology therefore appears to act mainly on the kinetics of postcritical growth rather than on T m. Changing the charge topology alone did not eliminate the freezing artifact in any of these models. This motivated us to examine the balance between the vdW and electrostatic interactions directly.
Mitigation of the Freezing Artifact by Rebalancing vdW and Electrostatic Interactions
The interaction between two polar CG water particles contains both vdW and electrostatic contributions, represented here by LJ and Coulomb potentials, respectively. The parameters ϵLJ and σLJ control the magnitude and length scale of the vdW interaction, whereas εbg scales the direct electrostatic interaction. These contributions must be adjusted jointly when density and surface tension are used as parametrization targets because both properties depend on the total nonbonded interaction.
Under the parametrization constraints of reproducing the experimental density and surface tension, the LJ parameters vary among models with different charge topologies, particularly in ϵLJ. The ϵLJ values of the four models span 0.895–1.050 kcal/mol, and their T m values increase monotonically over this range as shown in Figure (a), despite the differences in charge topology and LJ functional form. Across these independently parametrized models, the ordering of T m follows ϵLJ rather than the charge topology.
6.

(a) Operational melting temperature T m of the four CG water models as a function of their parametrized ϵLJ values. (b) Phase behavior at 273 K as a function of ϵLJ with 0.1 kcal/mol increments, and with all other force-field parameters held fixed. Red squares and blue circles indicate crystalline and liquid states, respectively.
To examine the role of the LJ attraction more directly, we performed solid–liquid coexistence simulations at 273 K for SPICA, pSPICA, p3SPICA-120, and p3SPICA-104.5 while varying ϵLJ and holding the other force-field parameters fixed. As shown in Figure (b), each model changed from liquid-like to crystalline behavior over a relatively narrow ϵLJ interval of approximately 0.7–0.9 kcal/mol, with p3SPICA-104.5 showing a slightly higher transition range. Under this specific protocol, ϵLJ = 0.7 kcal/mol therefore provides a practical lower-bound reference below which the liquid state was stable for all four models. This threshold was determined under the SPICA-family parametrization protocol, and its generality across other CG water models remains to be examined.
Nevertheless, the similar transition ranges across models with different charge representations indicate that the freezing behavior is highly sensitive to the LJ interaction strength. The parametrized ϵLJ values of the four original models lie above the liquid-stability reference identified in Figure (b), consistent with their high operational melting temperatures. Lowering ϵLJ toward this range should therefore mitigate freezing. To preserve the target density and surface tension while weakening the LJ attraction, the electrostatic contribution must be strengthened. With the dipole moment fixed at the AA-MD reference value of 4.4 D, we treat εbg as the parametrization variable that controls the weight of the electrostatic interaction within the total nonbonded interaction. Reducing εbg at a fixed dipole moment increases this electrostatic contribution and thereby permits a weaker LJ attraction, that is, a smaller ϵLJ.
On this basis, we developed the parametrization framework shown in Figure for introducing a permanent dipole into a nonpolar CG water model while reducing its freezing tendency. Following the framework, we began with nonpolar SPICA water and identified the threshold ϵLJ value for freezing, ϵthres, which is 0.7 kcal/mol for the SPICA family as shown earlier. We then introduced the fixed 4.4 D dipole used in the original pSPICA parametrization. Various combinations of ε bg, ϵLJ, and σLJ were then examined to quantify their relationships with the density and surface tension at 298 K. Over the parameter range examined, linear regressions were found to describe these local relationships adequately, as discussed in the Supporting Information. The fitted relations were used to identify parameter combinations that reproduced target values of ρ = 1 g/cm3 and γ = 72 mN/m at 298 K.
7.

Proposed parametrization framework for introducing polarity into a nonpolar CG water model while mitigating its freezing tendency.
With the LJ 12–5 functional form used in pSPICA, however, we were unable to reproduce both target properties after reducing ϵLJ close to ϵthres = 0.7 kcal/mol. We therefore adopted the LJ 12–4 form used in nonpolar SPICA. Its longer-ranged attractive component provided sufficient flexibility to reproduce the density and surface tension with a weaker well depth, as detailed in the Supporting Information.
Reducing εbg strengthens the explicit electrostatic interaction and thus permits a smaller ϵLJ while retaining the target liquid properties. To assess the associated freezing behavior, we performed coexistence simulations for parameter sets spanning a range of εbg values, with ϵLJ and σLJ predicted from the fitted property relationships. Figure shows a nonmonotonic dependence of the operational T m on εbg, with a minimum near εbg = 1.5. At larger εbg, a larger ϵLJ is required to maintain the density and surface tension, and T m rises sharply. At smaller εbg, the stronger electrostatic interaction may promote dipolar alignment or ordered packing, partially offsetting the benefit of the reduced LJ attraction and producing a modest increase in T m. Detailed mechanisms of dipolar ordering and its interplay with the LJ attraction during freezing would require further structural analysis, which is beyond the scope of the present parametrization study.
8.

Melting temperature (T m) as a function of the background dielectric constant εbg. At each εbg, the Lennard–Jones parameters (ϵLJ) and σLJ were selected using the established parameter-property correlations to reproduce the experimental density and surface tension at 298 K, following the parametrization framework shown in Figure .
The asymmetry of the T m curve indicates that, along the parametrization path examined, freezing is more sensitive to increases in ϵLJ than to comparable changes in εbg. We therefore selected εbg = 1.5 for pSPICA2. At this value, ϵLJ and σLJ were further refined to reproduce the density and surface tension at 298 K. Because r 0 altered εr while having only minor effects on ρ and γ over the examined range, r 0 and the partial charges Q WO and Q WH were then adjusted at a fixed dipole moment of 4.4 D to reproduce the target dielectric permittivity. The refinement of ϵLJ and σLJ, followed by adjustment of r 0 and the charges, was iterated until the target properties converged. The final pSPICA2 parameter set is listed in Table .
At 298 K, pSPICA2 reproduces the bulk density, surface tension, and dielectric permittivity to within approximately 1% of the experimental values (Table ). The surface-tension overestimation of the original pSPICA parametrization is largely removed, and the dielectric permittivity remains close to the experimental value. Figure shows that pSPICA2 also retains the overall temperature dependence of ρ(T) over 290–363 K. At the upper end of this range, its density decreases somewhat more steeply than that of pSPICA and deviates more from experiment, possibly reflecting the stronger electrostatic contribution at lower εbg. The γ(T) profile is reproduced well at low and intermediate temperatures. Thus, pSPICA2 preserves the principal temperature-dependent liquid properties of the SPICA family, although some high-temperature deviations remain.
The principal improvement is the substantially lower freezing tendency. The operational T m decreases from 384 K for pSPICA to 302 K for pSPICA2, although it remains 29 K above the experimental value and slightly above room temperature. We also performed 50 independent nucleation simulations at 240 K using the same protocol applied to the other models. Only one trajectory froze within the simulation time window, preventing reliable fitting of ΔG*, n*, or R G for pSPICA2 (Table ). Under the identical nucleation protocol, the fraction of trajectories that froze decreased from 50 out of 50 for SPICA, pSPICA, p3SPICA-120, and p3SPICA-104.5 to 1 out of 50 for pSPICA2, indicating a substantial kinetic suppression of freezing.
These results demonstrate that rebalancing the vdW and electrostatic contributions can substantially mitigate the freezing artifact in a polar CG water model while preserving its targeted thermodynamic and dielectric properties. The parametrization logic provides a practical starting point for related models, and its extension to other CG water models requires further testing in the future.
Conclusions
We systematically examined CG water models of the SPICA FF family with different charge topologies: the uncharged model (SPICA), the two-site linear dipole (pSPICA), and two three-site V-shaped charge distributions (p3SPICA-120 and p3SPICA-104.5). All polar models were parametrized to accurately reproduce the experimental density, surface tension, and dielectric permittivity at 298 K. This shows that an explicit dipole can be introduced and the LJ parameters can be refitted accordingly to match target water properties. Changes in charge topology were therefore necessarily associated with variations in the LJ parameters, and differences in the resulting properties reflected the combined effects of both. We also compared a mean-force-derived effective screening constant εeff with the dielectric permittivity εr obtained from equilibrium dipole fluctuations. The two measures were mutually consistent for the parameter sets examined, supporting the use of the fluctuation method as an operational dielectric measure for CG models with an explicit εbg. In addition, varying the dipole length r 0 at fixed dipole moment changed εr substantially while producing only small changes in density and surface tension over the tested range, providing a useful parametrization degree of freedom.
Despite the comparable ambient properties, the four models exhibited markedly different freezing behaviors. Particularly, under the parametrization constraints of density and surface tension, changing the charge topology from a linear dipole to a V-shaped distribution modified the freezing kinetics: the postcritical growth rate decreased from the nonpolar model to the linear dipole and then to the V-shaped geometries. Yet, changing the charge topology did not eliminate the freezing artifact as all tested polar models retained higher T m than nonpolar SPICA. Charge topology therefore affected mainly the kinetics of nucleus growth rather than the melting point itself. In contrast, T m across the four models was found to increase monotonically with the parametrized ϵLJ despite differences in charge topology and LJ functional form. When ϵLJ was varied in coexistence simulations, all four models showed a liquid-to-crystalline transition within a narrow interval near 0.7–0.9 kcal/mol under the same testing protocol. This indicates that T m is strongly sensitive to the LJ interaction strength, regardless of the charge topology or LJ functional form. This motivated us to rebalance the LJ and electrostatic contributions to mitigate the freezing artifact.
On the basis of these results, we proposed a framework that strengthens the explicit electrostatic contribution by reducing εbg and correspondingly weakens the LJ attraction while preserving target values of density, surface tension, and dielectric permittivity. The resulting pSPICA2 model reduced the operational T m from 384 K for pSPICA to 302 K. At 298 K, it retained a density of 1.003 g/cm3, a surface tension of 71.9 mN/m, and a dielectric permittivity of 79.1. It also reproduced the principal temperature dependence of density and surface tension over 290–363 K, although deviations remained at elevated temperatures. Under the same 240 K nucleation protocol used for the other models, the fraction of trajectories with freezing events decreased from 50 out of 50 for the four original models down to 1 out of 50 for pSPICA2.
The pSPICA2 model therefore mitigates rather than eliminates the freezing artifact, as its operational T m remains above the experimental value of 273 K while the freezing kinetics are substantially suppressed. Nevertheless, the present results show that polarity can be introduced into the SPICA water framework without retaining the full freezing tendency of the original pSPICA model. More broadly, the strategy of rebalancing electrostatic and vdW interactions may provide a useful starting point for developing other explicitly charged CG water models, provided that transferability, interfacial composition, dynamical properties, and compatibility with the surrounding force field are evaluated independently.
Supplementary Material
Acknowledgments
The authors thank the supports by the National Science and Technology Council of Taiwan (NSTC 113-2221-E-006-018-MY3, NSTC 114-2923-E-006-001, and NSTC 114-2639-M-400-001). WS acknowledges funding by JSPS Kakenhi Grant Numbers JP24H00843, JP25K01729, and JP26K22773. C.-c.C. also acknowledges the support by the Center of Resilience and Intelligence on Sustainable Energy Research (RiSER) of National Cheng Kung University, from the framework of the Higher Education Sprout Project by the Ministry of Education (MOE) in Taiwan.
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jpcb.6c06050.
Test sets of εbg, ϵLJ, σLJ, the corresponding water density ρ and surface tension γ at 298 K, and the resulting linear correlations; the ϵLJ and σLJ combinations at various εbg satisfying experimental ρ = 1 g/cm3 and γ = 72 mN/m predicted using the linear correlations (PDF)
#.
Fritz-Haber-Institute of the Max-Planck-Society, 14195 Berlin, Germany
The authors declare no competing financial interest.
Published as part of The Journal of Physical Chemistry B special issue “Computer Simulation of Molecular Solids and Liquids: In Honor of Michael L. Klein”.
References
- Klein M. L., Shinoda W.. Large-scale molecular dynamics simulations of self-assembling systems. Science. 2008;321:798–800. doi: 10.1126/science.1157834. [DOI] [PubMed] [Google Scholar]
- Shinoda W., DeVane R., Klein M. L.. Computer simulation studies of self-assembling macromolecules. Curr. Opin. Struct. Biol. 2012;22:175–186. doi: 10.1016/j.sbi.2012.01.011. [DOI] [PubMed] [Google Scholar]
- Marrink S. J., Monticelli L., Melo M. N., Alessandri R., Tieleman D. P., Souza P. C. T.. Two decades of Martini: Better beads, broader scope. WIREs Comput. Mol. Sci. 2023;13:e1620. doi: 10.1002/wcms.1620. [DOI] [Google Scholar]
- Khodadadi E., Khodadadi E., Chaturvedi P., Moradi M.. Molecular Dynamics Simulations of Liposomes: Structure, Dynamics, and Applications. Membranes. 2025;15:259. doi: 10.3390/membranes15090259. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Marrink S. J., Corradi V., Souza P. C., Ingólfsson H. I., Tieleman D. P., Sansom M. S.. Computational Modeling of Realistic Cell Membranes. Chem. Rev. 2019;119:6184–6226. doi: 10.1021/acs.chemrev.8b00460. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Marrink S. J., Risselada H. J., Yefimov S., Tieleman D. P., de Vries A. H.. The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations. J. Phys. Chem. B. 2007;111:7812–7824. doi: 10.1021/jp071097f. [DOI] [PubMed] [Google Scholar]
- Monticelli L., Kandasamy S. K., Periole X., Larson R. G., Tieleman D. P., Marrink S.-J.. The MARTINI Coarse-Grained Force Field: Extension to Proteins. J. Chem. Theory Comput. 2008;4:819–834. doi: 10.1021/ct700324x. [DOI] [PubMed] [Google Scholar]
- Souza P. C. T., Alessandri R., Barnoud J., Thallmair S., Faustino I., Grünewald F., Patmanidis I., Abdizadeh H., Bruininks B. M. H., Wassenaar T. A., Kroon P. C., Melcr J., Nieto V., Corradi V., Khan H. M., Domański J., Javanainen M., Martinez-Seara H., Reuter N., Best R. B., Vattulainen I., Monticelli L., Periole X., Tieleman D. P., de Vries A. H., Marrink S. J.. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nat. Methods. 2021;18:382–388. doi: 10.1038/s41592-021-01098-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Grünewald F., Punt M. H., Jefferys E. E., Vainikka P. A., König M., Virtanen V., Meyer T. A., Pezeshkian W., Gormley A. J., Karonen M., Sansom M. S. P., Souza P. C. T., Marrink S. J.. Martini 3 Coarse-Grained Force Field for Carbohydrates. J. Chem. Theory Comput. 2022;18:7555–7569. doi: 10.1021/acs.jctc.2c00757. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pedersen K. B., Ingólfsson H. I., Ramirez-Echemendia D. P., Borges-Araújo L., Andreasen M. D., Empereur-mot C., Melcr J., Ozturk T. N., Bennett W. F. D., Kjølbye L. R., Brasnett C., Corradi V., Khan H. M., Cino E. A., Crowley J., Kim H., Fábián B., Borges-Araújo A. C., Pavan G. M., Launay G., Lolicato F., Wassenaar T. A., Melo M. N., Thallmair S., Carpenter T. S., Monticelli L., Tieleman D. P., Schiøtt B., Souza P. C. T., Marrink S. J.. The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior. ACS Cent. Sci. 2025;11:1598–1610. doi: 10.1021/acscentsci.5c00755. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Borges-Araújo L., Pereira G. P., Valério M., Souza P. C.. Assessing the Martini 3 protein model: A review of its path and potential. Biochim. Biophys. Acta, Proteins Proteomics. 2024;1872:141014. doi: 10.1016/j.bbapap.2024.141014. [DOI] [PubMed] [Google Scholar]
- Wang L., Brasnett C., Borges-Araújo L., Souza P. C. T., Marrink S. J.. Martini3-IDP: improved Martini 3 force field for disordered proteins. Nat. Commun. 2025;16:2874. doi: 10.1038/s41467-025-58199-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shinoda W., DeVane R., Klein M. L.. Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants. Mol. Simul. 2007;33:27–36. doi: 10.1080/08927020601054050. [DOI] [Google Scholar]
- Shinoda W., DeVane R., Klein M. L.. Coarse-grained molecular modeling of non-ionic surfactant self-assembly. Soft Matter. 2008;4:2454–2462. doi: 10.1039/b808701f. [DOI] [Google Scholar]
- Shinoda W., DeVane R., Klein M. L.. Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field. J. Phys. Chem. B. 2010;114:6836–6849. doi: 10.1021/jp9107206. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shinoda W., DeVane R., Klein M. L.. Coarse-grained force field for ionic surfactants. Soft Matter. 2011;7:6178–6186. doi: 10.1039/c1sm05173c. [DOI] [Google Scholar]
- Seo S., Shinoda W.. SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol. J. Chem. Theory Comput. 2019;15:762–774. doi: 10.1021/acs.jctc.8b00987. [DOI] [PubMed] [Google Scholar]
- Kawamoto S., Liu H., Miyazaki Y., Seo S., Dixit M., DeVane R., MacDermaid C., Fiorin G., Klein M. L., Shinoda W.. SPICA Force Field for Proteins and Peptides. J. Chem. Theory Comput. 2022;18:3204–3217. doi: 10.1021/acs.jctc.1c01207. [DOI] [PubMed] [Google Scholar]
- Yamada T., Miyazaki Y., Harada S., Kumar A., Vanni S., Shinoda W.. Improved Protein Model in SPICA Force Field. J. Chem. Theory Comput. 2023;19:8967–8977. doi: 10.1021/acs.jctc.3c01016. [DOI] [PubMed] [Google Scholar]
- Singh A. P., Tanaka H., Miyazaki Y., Shinoda W.. SPICA Force Field for Nucleic Acids and Its Application to Lipid Nanoparticles. J. Phys. Chem. B. 2025;129:7939–7950. doi: 10.1021/acs.jpcb.5c01729. [DOI] [PubMed] [Google Scholar]
- Seo S., Murata M., Shinoda W.. Pivotal Role of Interdigitation in Interleaflet Interactions: Implications from Molecular Dynamics Simulations. J. Phys. Chem. Lett. 2020;11:5171–5176. doi: 10.1021/acs.jpclett.0c01317. [DOI] [PubMed] [Google Scholar]
- Yamada T., Shinoda W.. Asymmetry and Heterogeneity in the Plasma Membrane. Biophys. J. 2026;125:387–395. doi: 10.1016/j.bpj.2025.06.026. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Singh S. K., Noroozi A., Soldera A.. Coarse-grained simulation of water: A comparative study and overview. J. Chem. Phys. 2025;162:144501. doi: 10.1063/5.0249333. [DOI] [PubMed] [Google Scholar]
- Zavadlav J., Arampatzis G., Koumoutsakos P.. Bayesian selection for coarse-grained models of liquid water. Sci. Rep. 2019;9:99. doi: 10.1038/s41598-018-37471-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Onufriev A. V., Izadi S.. Water models for biomolecular simulations. WIREs Comput. Mol. Sci. 2018;8:e1347. doi: 10.1002/wcms.1347. [DOI] [Google Scholar]
- Ding W., Palaiokostas M., Orsi M.. Stress testing the ELBA water model. Mol. Simul. 2016;42:337–346. doi: 10.1080/08927022.2015.1047367. [DOI] [Google Scholar]
- Hadley K. R., McCabe C.. Coarse-grained molecular models of water: a review. Mol. Simul. 2012;38:671–681. doi: 10.1080/08927022.2012.671942. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Darré L., Machado M. R., Pantano S.. Coarse-grained models of water. WIREs Comput. Mol. Sci. 2012;2:921–930. doi: 10.1002/wcms.1097. [DOI] [Google Scholar]
- Yesylevskyy S. O., Schäfer L. V., Sengupta D., Marrink S. J.. Polarizable Water Model for the Coarse-Grained MARTINI Force Field. PLos Comput. Biol. 2010;6:e1000810. doi: 10.1371/journal.pcbi.1000810. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Miyazaki Y., Okazaki S., Shinoda W.. pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model. J. Chem. Theory Comput. 2020;16:782–793. doi: 10.1021/acs.jctc.9b00946. [DOI] [PubMed] [Google Scholar]
- Jorgensen W. L., Chandrasekhar J., Madura J. D., Impey R. W., Klein M. L.. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983;79:926–935. doi: 10.1063/1.445869. [DOI] [Google Scholar]
- Duarte F., Bauer P., Barrozo A., Amrein B. A., Purg M., Åqvist J., Kamerlin S. C. L.. Force Field Independent Metal Parameters Using a Nonbonded Dummy Model. J. Phys. Chem. B. 2014;118:4351–4362. doi: 10.1021/jp501737x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wu Z., Cui Q., Yethiraj A.. A New Coarse-Grained Model for Water: The Importance of Electrostatic Interactions. J. Phys. Chem. B. 2010;114:10524–10529. doi: 10.1021/jp1019763. [DOI] [PubMed] [Google Scholar]
- Riniker S., van Gunsteren W. F.. A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations. J. Chem. Phys. 2011;134:084110. doi: 10.1063/1.3553378. [DOI] [PubMed] [Google Scholar]
- Orsi M., Essex J. W.. The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes. PLoS One. 2011;6:e28637. doi: 10.1371/journal.pone.0028637. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Orsi M.. Comparative assessment of the ELBA coarse-grained model for water. Mol. Phys. 2014;112:1566–1576. doi: 10.1080/00268976.2013.844373. [DOI] [Google Scholar]
- Braun D., Boresch S., Steinhauser O.. Transport and dielectric properties of water and the influence of coarse-graining: Comparing BMW, SPC/E, and TIP3P models. J. Chem. Phys. 2014;140:064107. doi: 10.1063/1.4864117. [DOI] [PubMed] [Google Scholar]
- Miyazaki Y., Shinoda W.. pSPICA Force Field Extended for Proteins and Peptides. J. Chem. Inf. Model. 2024;64:532–542. doi: 10.1021/acs.jcim.3c01611. [DOI] [PubMed] [Google Scholar]
- Wu Z., Cui Q., Yethiraj A.. A New Coarse-Grained Force Field for Membrane-Peptide Simulations. J. Chem. Theory Comput. 2011;7:3793–3802. doi: 10.1021/ct200593t. [DOI] [PubMed] [Google Scholar]
- Wu Z., Cui Q., Yethiraj A.. Driving Force for the Association of Hydrophobic Peptides: The Importance of Electrostatic Interactions in Coarse-Grained Water Models. J. Phys. Chem. Lett. 2011;2:1794–1798. doi: 10.1021/jz2006622. [DOI] [Google Scholar]
- Winger M., Trzesniak D., Baron R., van Gunsteren W. F.. On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. Phys. Chem. Chem. Phys. 2009;11:1934–1941. doi: 10.1039/b818713d. [DOI] [PubMed] [Google Scholar]
- He X., Shinoda W., DeVane R., Klein M. L.. Exploring the utility of coarse-grained water models for computational studies of interfacial systems. Mol. Phys. 2010;108:2007–2020. doi: 10.1080/00268976.2010.503197. [DOI] [Google Scholar]
- Iannetti L., Cambiaso S., Rasera F., Giacomello A., Rossi G., Bochicchio D., Tinti A.. The surface tension of Martini 3 water mixtures. J. Chem. Phys. 2024;161:084707. doi: 10.1063/5.0221199. [DOI] [PubMed] [Google Scholar]
- Humphrey W., Dalke A., Schulten K.. VMD: visual molecular dynamics. J. Mol. Graphics. 1996;14:33–38. doi: 10.1016/0263-7855(96)00018-5. [DOI] [PubMed] [Google Scholar]
- Hockney, R. W. ; Eastwood, J. W. . Computer Simulation Using Particles; CRC Press, 1988. [Google Scholar]
- Neumann M.. Dipole moment fluctuation formulas in computer simulations of polar systems. Mol. Phys. 1983;50:841–858. doi: 10.1080/00268978300102721. [DOI] [Google Scholar]
- Ryckaert J.-P., Ciccotti G., Berendsen H. J. C.. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977;23:327–341. doi: 10.1016/0021-9991(77)90098-5. [DOI] [Google Scholar]
- Plimpton S.. Fast parallel algorithms for short-range molecular dynamics. J. Comput. Phys. 1995;117:1–19. doi: 10.1006/jcph.1995.1039. [DOI] [Google Scholar]
- Thompson A. P., Aktulga H. M., Berger R., Bolintineanu D. S., Brown W. M., Crozier P. S., in ’t Veld P. J., Kohlmeyer A., Moore S. G., Nguyen T. D., Shan R., Stevens M. J., Tranchida J., Trott C., Plimpton S. J.. LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Comput. Phys. Commun. 2022;271:108171. doi: 10.1016/j.cpc.2021.108171. [DOI] [Google Scholar]
- Nosé S.. A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys. 1984;81:511–519. doi: 10.1063/1.447334. [DOI] [Google Scholar]
- Hoover W. G.. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A. 1985;31:1695–1697. doi: 10.1103/PhysRevA.31.1695. [DOI] [PubMed] [Google Scholar]
- Parrinello M., Rahman A.. Polymorphic transitions in single crystals: A new molecular dynamics. J. Appl. Phys. 1981;52:7182–7190. doi: 10.1063/1.328693. [DOI] [Google Scholar]
- Fernández R. G., Abascal J. L. F., Vega C.. The melting point of ice Ih for common water models calculated from direct coexistence of the solid-liquid interface. J. Chem. Phys. 2006;124:144506. doi: 10.1063/1.2183308. [DOI] [PubMed] [Google Scholar]
- ten Wolde P. R., Ruiz-Montero M. J., Frenkel D.. Simulation of homogeneous crystal nucleation close to coexistence. Faraday Discuss. 1996;104:93–110. doi: 10.1039/fd9960400093. [DOI] [Google Scholar]
- Rein ten Wolde P., Ruiz-Montero M. J., Frenkel D.. Numerical calculation of the rate of crystal nucleation in a Lennard-Jones system at moderate undercooling. J. Chem. Phys. 1996;104:9932–9947. doi: 10.1063/1.471721. [DOI] [Google Scholar]
- Steinhardt P. J., Nelson D., Ronchetti M.. Bond-orientational order in liquids and glasses. Phys. Rev. B. 1983;28:784. doi: 10.1103/PhysRevB.28.784. [DOI] [Google Scholar]
- Ramasubramani V., Dice B. D., Harper E. S., Spellings M. P., Anderson J. A., Glotzer S. C.. freud: A software suite for high throughput analysis of particle simulation data. Comput. Phys. Commun. 2020;254:107275. doi: 10.1016/j.cpc.2020.107275. [DOI] [Google Scholar]
- Chkonia G., Wölk J., Strey R., Wedekind J., Reguera D.. Evaluating nucleation rates in direct simulations. J. Chem. Phys. 2009;130:064505. doi: 10.1063/1.3072794. [DOI] [PubMed] [Google Scholar]
- Wedekind J., Strey R., Reguera D.. New method to analyze simulations of activated processes. J. Chem. Phys. 2007;126:134103. doi: 10.1063/1.2713401. [DOI] [PubMed] [Google Scholar]
- Yuhara D., Barnes B. C., Suh D., Knott B. C., Beckham G. T., Yasuoka K., Wu D. T., Sum A. K.. Nucleation rate analysis of methane hydrate from molecular dynamics simulations. Faraday Discuss. 2015;179:463–474. doi: 10.1039/C4FD00219A. [DOI] [PubMed] [Google Scholar]
- Lide, D. CRC Handbook of Chemistry and Physics, 88th ed.; CRC Press/Taylor & Francis, 2007. [Google Scholar]
- Chiacchiera S., Warren P. B., Masters A. J., Seaton M. A.. Coarse-grained polarizable soft solvent models, with applications in dissipative particle dynamics. J. Chem. Phys. 2024;161:174115. doi: 10.1063/5.0226871. [DOI] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
