Constant Temperature Ensemble Research Articles

Performance Tuning of Polarizable Gaussian Multipole Model in Molecular Dynamics Simulations.

Molecular dynamics (MD) simulations are essential for understanding molecular phenomena at the atomic level, with their accuracy largely dependent on both the employed force field and sampling. Polarizable force fields, which incorporate atomic polarization effects, represent a significant advancement in simulation technology. The polarizable Gaussian multipole (pGM) model has been noted for its accurate reproduction of ab initio electrostatic interactions. In this study, we document our effort to enhance the computational efficiency and scalability of the pGM simulations within the AMBER framework using MPI (message passing interface). Performance evaluations reveal that our MPI-based pGM model significantly reduces runtime and scales effectively while maintaining computational accuracy. Additionally, we investigated the stability and reliability of the MPI implementation under the NVE simulation ensemble. Optimal Ewald and induction parameters for the pGM model are also explored, and its statistical properties are assessed under various simulation ensembles. Our findings demonstrate that the MPI-implementation maintains enhanced stability and robustness during extended simulation times. We further evaluated the model performance under both NVT (constant number, volume, and temperature) and NPT (constant number, pressure, and temperature) ensembles and assessed the effects of varying timesteps and convergence tolerance on induced dipole calculations. The lessons learned from these exercises are expected to help the users to make informed decisions on simulation setup. The improved performance under these ensembles enables the study of larger molecular systems, thereby expanding the applicability of the pGM model in detailed MD simulations.

Diffusivity of individual adsorbed water molecules at an Fe2O3 − Hematite/Water interface under external electric-field conditions

The dynamical properties of physically and chemically adsorbed water molecules at a pristine hematite-(001) surfaces have been studied by non-equilibrium ab-initio molecular dynamics in the constant-volume, constant-temperature ensemble at room temperature, under externally-applied, uniform static electric fields of increasing intensity. Significant alterations in the dipole moment and self-diffusion constant were found vis-à-vis zero-field conditions, as well as shifting of the probability distribution of individual molecular self-diffusivities. For instance, application of static fields was found to increase the self-diffusion of water molecules at the α-hematite Fe2O3 surface, effectively due to some extent of ‘dipole-locking’ in the direction of the applied field.

Mass-zero constrained dynamics for simulations based on orbital-free density functional theory.

A new algorithm for efficient and fully time-reversible integration of first-principles molecular dynamics based on orbital-free density functional theory (OFDFT) is presented. The algorithm adapts to this nontrivial case, the recently introduced Mass-Zero (MaZe) constrained dynamics. The formalism ensures that full adiabatic separation is enforced between nuclear and electronic degrees of freedom and, consequently, that the exact Born-Oppenheimer probability for the nuclei is sampled. Numerical integration of the MaZe dynamics combines standard molecular dynamics algorithms, e.g., Verlet or velocity Verlet, with the SHAKE method to impose the minimum conditions on the electronic degrees of freedom as a set of constraints. The developments presented in this work, which include a bespoke adaptation of the standard SHAKE algorithm, ensure that the quasilinear scaling of OFDFT is preserved by the new method for a broad range of kinetic and exchange-correlation functionals, including nonlocal ones. The efficiency and accuracy of the approach are demonstrated via calculations of static and dynamic properties of liquid sodium in the constant energy and constant temperature ensembles.

Enhanced thermophysical properties of water-based single and hybrid metallic nanofluids: Insights from Equilibrium Molecular Dynamics

The effect of single (Cu or Ag) and hybrid (Cu+Ag) metallic nanoparticles on the thermophysical properties, namely viscosity and thermal conductivity of water-based nanofluids, has been studied using Equilibrium Molecular dynamics (EMD) simulation. The TIP3P (three-site transferrable intermolecular potential) water model has been chosen. The interaction of water molecules has been modelled by the Lennard-Jones (L J) potential in combination with Coulomb potential. The embedded-atom (EAM) potential method has been used for hybrid (Cu and Ag) atom interaction. Simulation has been performed at 303 K and atmospheric pressure using the Berendsen algorithm under NVT (constant number, constant volume, and constant temperature) ensemble with production steps of 2 ns and integral step of 1fs. Interestingly, nanofluids containing one metallic nanoparticle (Cu or Ag) have lower thermal conductivity and viscosity than nanofluids having hybrid metallic nanoparticles with the same volume fraction.

Molecular dynamics simulation of bamboo heat treatment with cellulose based on molecular different weight fractions of water

Eight groups of cellulose amorphous region models in which the mass fraction of water was separately 0%, 1%, 2%, 3%, 4%, 5%, 6%, and 7% were established using a molecular dynamics software material studio. The PCFF force field was selected to simulate the molecular dynamics of the model under the constant-pressure and constant-temperature (NPT) ensemble. The simulated temperature was set to 433.15 K. The experiment showed that the hydrogen bonds between cellulose chains affected the structure of cellulose, which led to the change of the end-to-end distance of the cellulose chain and the overall size of a cell. The diffusion degree of water molecules was closely related to the number of hydrogen bonds between cellulose and water. In the process of heat treatment of bamboo, the present simulation results suggest that the structure of bamboo may be damaged when the mass fraction of water vapor reaches or exceeds 7%.

Interaction study between M-Phenylenediamine, Trimesoyl Chloride and Nylon 66 using Molecular Dynamic Simulation

The thin film composite (TFC) membrane is a porous membrane layered by a polyamide active layer. In the experimental work, the polyamide active layer prepared by the interaction between monomers, m-phenylenediamine (MPD) and trimesoyl chloride (TMC) which deposited on a membrane support. Considering the possibility of producing a loose TFC membrane and affect the separation performance, this study enlightens the interaction between monomers with Nylon 6 6 (N66) support membrane using simulation - molecular dynamic (MD). Different simulation system has been investigated with varying the ratio molecule of MPD to TMC where, TFC1 (1:1), TFC2 (3:1) and TFC3 (3:2) to the tertiary system of N66/MPD/TMC. The simulation was set for a COMPASS force field, where the equilibrium phases in a microcanonical (constant volumes and total energy) (NVE) followed by run-production stage (constant pressure and temperature ensembles) (NPT) ensembles. The temperature and pressure were set at 323.15 K and 1atm respectively. The polyamide TFC was found to be formed by the main interactions between nitrogen (N) from MPD group to the carbon, (C) from TMC main chain at ranges of 4.25Å. Overall interaction can be observed between N from TFC layer with O atom from the substrate layer. All of the intermolecular interactions take place at 3.25Å distance. The best interaction in N66 to MPD and TMC system to the weakest is in the arrangement of TFC2 > TFC3 > TFC1. The highest intensity was obtained by the TFC2, indicating the best ratio of 3:1 of MPD molecules to TMC molecule with support polymer when fully polymerized occurred. This study suggests that ratio N66 to MPD and TMC in TFC2 is the best to interaction between TFC layer and substrate for fabrication of the TFC membrane.

Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations

Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure–constant temperature ensemble. These materials exhibit a distinct “smectic” liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications.

Thermal Stability of Single Walled SiGe Nanotube with Vacancy Defects: a Molecular Dynamics Simulation Study

The aim of this investigation was to study thermal properties of perfect and imperfect single-walled Si-x%Ge (atomic percentages) armchair nanotubes. We have performed molecular dynamics simulation computations based on Tersoff many body potential in the constant temperature and pressure ensemble. The temperature and pressure of the nanotube were controlled by a Nose-Hoover thermostat and barostat, respectively. The phase diagram of the Si-x%Ge nanotube was built by changing atomic percentages of Ge and then melting the nanotube. Our results show that cohesive energy increases, isobaric heat capacity, and thermal stability of Si-x%Ge nanotube decrease with increasing Ge composition in the nanotube. Moreover, we created 0.5, 1, 1.5, …, 4 at% vacancy defects in the nanotubes to study thermal properties of imperfect Si-Ge nanotubes. Finally, the average of formation energy per defect was calculated as 0.39 eV by MD simulation.

SEED CONCENTRATION EFFECT ON HETEROGENEOUS NUCLEATION BY MOLECULAR DYNAMICS

Heterogeneous nucleation on a system with multiple seeds were conducted by molecular dynamics to understand how seed concentrations can affect the phase transition process. A constant particle number, volume, and temperature ensemble was applied to multiple systems of Lennard-Jones particles with a carrier gas that acts as a thermal reservoir. A different number of seeds were inserted into systems that have been previously found to have no spontaneous nucleation due to low supersaturation ratios. The addition of the seeds activated nucleation, but the increase in the nucleation rate was not perpetual because the system size was finite. A clear understanding of how the number of seeds decreasing the free energy barrier is presented along with the kinetic attachment and detachment rate variations. The decrease in the free energy barrier has a limit similarly to the aforementioned nucleation rate increase. The seed concentration results coincide with the predictions from the classical nucleation theory.

Geometric ergodicity of two-dimensional Hamiltonian systems with a Lennard–Jones-like repulsive potential

Molecular dynamics simulation is among the most important and widely used tools in the study of molecular systems, providing fundamental insights into molecular mechanisms at a level of detail unattainable by experimental methods [AT87, Lea96, FS96, Sch02]. Usage of molecular dynamics spans a diverse array of fields, from physics and chemistry, to molecular and cellular biology, to engineering and materials science. Due to their size and complexity, simulations of large systems such as biological macromolecules (DNA, RNA, proteins, carbohydrates, and lipids) are typically performed under a classical mechanics representation. A critical requirement of such simulations is ergodicity, or convergence in the limit to the equilibrium (typically canonical) Boltzmann measure μ(dq, dp) = Z(β)−1e−βH(q,p)dqdp. Although ergodicity is commonly assumed, recently [CS08] showed that all commonly used deterministic dynamics methods for simulating the canonical (constanttemperature) ensemble fail to be ergodic. They also showed that introduction of a stochastic hybrid Monte Carlo (HMC) correction guarantees ergodicity; however, HMC scales poorly with system dimension and is rarely used for macromolecules. [CS08] also show empirically that more commonly used stochastic Langevin dynamics [Pas94] appear to exhibit ergodic behavior, but were unable to provide rigorous proof. The key difficulty in applying existing arguments [MSH02] is the appearance of singularities in the potential U(q). Most modern molecular mechanics forcefields [PCC95, BBO83, JTR88] take the form

Molecular docking and molecular dynamics simulation analyses of urea with ammoniated and ammoxidized lignin

Ammoniated lignin, prepared through the Mannich reaction of lignin, has more advantages as a slow-release carrier of urea molecules than ammoxidized lignin and lignin. The advantages of the ammoniated lignin include its amine groups added and its high molecular mass kept as similar as that of lignin. Three organic molecules including guaiacyl, 2-hydroxybenzylamine and 5-carbamoylpentanoic acid are monomers respectively in lignin, ammoniated lignin and ammoxidized lignin. We studied the difference between the interactions of lignin, ammoniated lignin and ammoxidized lignin with respect to urea, based on radial distribution functions (RDFs) results from molecular dynamics (MD) simulations. Glass transition temperature (Tg) and solubility parameter (δ) of ammoniated and ammoxidized lignin have been calculated by MD simulations in the constant-temperature and constant-pressure ensemble (NPT). Molecular docking results showed the interaction sites of the urea onto the ammoniated and ammoxidized lignin and three different interaction modes were identified. Root mean square deviation (RMSD) values could indicate the mobilities of the urea molecule affected by the three different interaction modes. A series of MD simulations in the constant-temperature and constant-volume ensemble (NVT) helped us to calculate the diffusivity of urea which was affected by the content of urea in ammoniated and ammoxidized lignin.

Heterogeneous nucleation of bubbles by molecular dynamics

A homogeneous liquid system and a heterogeneous system with an impurity inserted inside it were used for investigation of bubble nucleation by molecular dynamics simulation. A constant particle number, volume, and temperature ensemble was used. The systems with the impurities showed an overall increase in bubble formation, which is consistent with previous studies. The shape of the impurities was changed to see if there was any direct influence on the bubble nucleation rate. With the limited number of systems investigated, the occurrence of a shape effect was inconclusive. As observed in previous heterogeneous nucleation studies with walls, the bubble initially forms remotely from the impurity and remains at some distance from the seed.

A simple molecular mechanics integrator in mixed rigid body and dihedral angle space.

We propose a numerical scheme to integrate equations of motion in a mixed space of rigid-body and dihedral angle coordinates. The focus of the presentation is biomolecular systems and the framework is applicable to polymers with tree-like topology. By approximating the effective mass matrix as diagonal and lumping all bias torques into the time dependencies of the diagonal elements, we take advantage of the formal decoupling of individual equations of motion. We impose energy conservation independently for every degree of freedom and this is used to derive a numerical integration scheme. The cost of all auxiliary operations is linear in the number of atoms. By coupling the scheme to one of two popular thermostats, we extend the method to sample constant temperature ensembles. We demonstrate that the integrator of choice yields satisfactory stability and is free of mass-metric tensor artifacts, which is expected by construction of the algorithm. Two fundamentally different systems, viz., liquid water and an α-helical peptide in a continuum solvent are used to establish the applicability of our method to a wide range of problems. The resultant constant temperature ensembles are shown to be thermodynamically accurate. The latter relies on detailed, quantitative comparisons to data from reference sampling schemes operating on exactly the same sets of degrees of freedom.

Molecular dynamics simulations of organic crystal dissolution: The lifetime and stability of the polymorphic forms of para-amino benzoic acid in aqueous environment

Para-amino benzoic acid (PABA) manifests crystalline solid-state properties that are typical of a class of chemical compounds with important industrial applications. Hence, it is particularly worthwhile to investigate the lifetime and stability of representative molecular-clusters of two polymorphic forms of PABA in aqueous solution using molecular dynamics simulations. Simulations of 5ns duration in the isothermal–isobaric ensemble (constant particle number, pressure and temperature (NPT) ensemble) were performed for the two polymorphic forms at three different temperatures 0°C, 50°C and 100°C. The simulations revealed that at 0°C the representative molecular-clusters of the two polymorphic forms remain ordered while at 50°C the molecular packing within the clusters becomes partially disordered for both polymorphic forms and at 100°C the clusters lose long-range order rapidly and come to resemble liquid drops. Care should be taken when assessing the relative stability of polymorphic forms, as a function of temperature, from such computational experiments which explore the dissolution of nano-scale crystals. The long range order of the clusters of the α-form at 50°C and 100°C was, respectively, partially and completely lost after 5ns which merits further investigation given that the α-form is the high-temperature stable polymorph. Importantly, the initial shape of clusters, as well as the number of solute molecules they contained, affected the extent to which order was lost and how rapidly the loss occurred. Given that the classical nucleation theory predicts a finite probability that clusters significantly larger than the critical size, in terms of number of molecules, may dissolve, building clusters containing a greater number of molecules could improve the simulated stability of the α polymorph at 50°C and 100°C. Furthermore, the simulations revealed that the selection of a suitable electrostatic potential is very important for the description of the dissolution process of the nano-sized crystals.

Identifying Key Amino Acid Residues That Affect α-Conotoxin AuIB Inhibition of α3β4 Nicotinic Acetylcholine Receptors

α-Conotoxin AuIB is a selective α3β4 nicotinic acetylcholine receptor (nAChR) subtype inhibitor. Its analgesic properties are believed to result from it activating GABAB receptors and subsequently inhibiting CaV2.2 voltage-gated calcium channels. The structural determinants that mediate diverging AuIB activity at these targets are unknown. We performed alanine scanning mutagenesis of AuIB and α3β4 nAChR, homology modeling, and molecular dynamics simulations to identify the structural determinants of the AuIB·α3β4 nAChR interaction. Two alanine-substituted AuIB analogues, [P6A]AuIB and [F9A]AuIB, did not inhibit the α3β4 nAChR. NMR and CD spectroscopy studies demonstrated that [F9A]AuIB retains its native globular structure, so its activity loss is probably due to loss of specific toxin-receptor residue pairwise contacts. Compared with AuIB, the concentration-response curve for inhibition of α3β4 by [F9A]AuIB shifted rightward more than 10-fold, and its subtype selectivity profile changed. Homology modeling and molecular dynamics simulations suggest that Phe-9 of AuIB interacts with a two-residue binding pocket on the β4 nAChR subunit. This hypothesis was confirmed by site-directed mutagenesis of the β4-Trp-59 and β4-Lys-61 residues of loop D, which form a putative binding pocket. AuIB analogues with Phe-9 substitutions corroborated the finding of a binding pocket on the β4 subunit and gave further insight into how AuIB Phe-9 interacts with the β4 subunit. In summary, we identified critical residues that mediate interactions between AuIB and its cognate nAChR subtype. These findings might help improve the design of analgesic conopeptides that selectively "avoid" nAChR receptors while targeting receptors involved with nociception.

Improved Charmm Force Field for Polyunsaturated Fatty Acid Chains, a Study on DAPC Membranes

The present research is a part of a collaborative effort to improve the CHARMMi force field (FF) parameters, referred to as C36p, for accurate prediction of the properties of polyunsaturated fatty acid (PUFA) chains in lipid membranes. The focus of our study was to test the accuracy of C36p FF. Molecular dynamics (MD) simulations were used to study the behavior of 1,2-diarachidonyl-phosphatidylcholine (DAPC), a PUFA with two hydrophobic tails with identical degree of unsaturation. CHARMM and NAMDii software packages were used to equilibrate and analyze the bilayer systems. The system consisted of a DAPC bilayer formed by 72 fully hydrated lipids with periodic boundary conditions. The simulations were performed in the NPT (constant particle number, pressure, and temperature) ensemble at 1 bar and 323.15 K for 100 ns. Simulations with the C36p FF resulted in more accurate membrane properties such as surface area per lipid, deuterium order parameters, electron density profiles, and C-H spin-lattice relaxation times.iii Efforts continue to improve the FF for accurate prediction on the rigidity of PUFA lipid membranes and orientation of cholesterol within these bilayers.EndnotesiCHARMM(Chemistry ar HARvard Macromolecular Mechanics). http://www.charmm.orgiiNAMD, Scalable Molecular Dynamics. http://www.ks.uiuc.edu/Research/namd/iiiKlauda, J.B.; Monje, V; Kim, T; Im, W. Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains. J. Phys. Chem, 2012, 116, 9424−9431.

Grain size dependence of the martensitic transformation in a nano-grained Fe–Ni polycrystal – A molecular dynamics study

Martensitic transformation (MT) in Fe–Ni binary alloys shows grain size dependence, which is an unresolved issue. Experimental results of MT in nano particles or nano-grained polycrystals are somehow controversial. Alternatively, computer simulation, e.g. molecular dynamics (MD) is becoming an important way which may give insight into the kinetics of phase transformations. Here MD simulation is applied to the study on grain size dependence of MT in nano-grained Vorononi construction polycrystalline systems by means of rapid quenching process in the constant temperature and stress (NPT) ensemble. Results show that the decrease of grain size would restrain MT in Fe(1−x)Nix (x=0.35, 0.25 and 0.15) alloy with the grain size from 5 to 15nm. The possible mechanism of grain size dependence is discussed based on both experimental and theoretical results.

Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains

CHARMM36 (C36) is the most up-to-date pairwise additive all-atom lipid force field and is able to accurately represent bilayer properties of saturated and monounsaturated lipid molecules in the natural constant particle, pressure, and temperature (NPT) ensemble. However, molecular dynamics (MD) simulations on 1-stearoyl-2-docosahexaenoyl-sn-glycerco-3-phosphocholine (SDPC) bilayers of the polyunsaturated fatty acid (PUFA) chains result in inaccuracies of the surface area per lipid (SA), deuterium order parameters (S(CD)), and X-ray form factors. Therefore, in this study, high-level quantum mechanical calculations are used to improve the dihedral potential of neighboring double bonds, and the corresponding force field is referred to as C36p. The SA for SDPC at 303 K increases from 63.2 ± 0.2 (C36) to 70.8 ± 0.2 (C36p) Å(2) and agrees favorably with X-ray diffraction results at 297 K. The resulting S(CD) are in excellent agreement with experimental values of both the sn-1 and sn-2 chains. Calculated NMR (13)C relaxation times and X-ray form factors from MD simulations of SDPC bilayers also agree with experiments. MD simulations of 1,2-diarachidonyl-phosphatidylcholine (DAPC) bilayers are used to further validate our force field parameters on a lipid with both chains containing PUFAs. As expected, the thickness of DAPC bilayers is reduced, and the SA is increased compared to the SDPC bilayers. This update in the PUFA force field should allow for accurate MD simulations of PUFA-containing bilayers in the NPT ensemble.

Loading Rate Effects on Mechanical Response of Ag, Ni, Al and Cu at Nano‐Scale

Abstract: Molecular dynamics (MD) is now playing a unique as well as conspicuous role in probing in nano‐science and technology. In this paper, MD simulation of uniaxial tension of some face‐centred cubic (FCC) metals (namely, Ag, Ni, Al and Cu) at nano‐scale was carried out. The effects of different loading rates on the stress–strain curves at a constant temperature of 300 K were studied. The potential used in these simulations was Sutton–Chen, and Velocity Verlet formulation of Noise‐Hoover dynamic was also applied to have a constant temperature ensemble. The boundary condition was periodic. Eventually, MD simulations were carried out and it was concluded that by increasing the loading rate both maximum stress and strain at failure increase. The maximum engineering stress for Al, Ag, Cu and Ni can be rounded as 4, 9, 12 and 18 GPa, respectively, for all loading rates.

Analysis of Dynamic Heterogeneity in a Glass Former from the Spatial Correlations of Mobility

The growth of characteristic length scales associated with dynamic heterogeneity in glass-forming liquids is investigated in an extensive computational study of a four-point, time-dependent structure factor defined from spatial correlations of mobility, for a model liquid for system sizes extending up to 351 232 particles, in constant-energy and constant-temperature ensembles. Our estimates for dynamic correlation lengths and susceptibilities are consistent with previous results from finite size scaling. We find scaling exponents that are inconsistent with predictions from inhomogeneous mode coupling theory and a recent simulation confirmation of these predictions.