Bond Force Field Research Articles

Type Label Framework for Bonded Force Fields in LAMMPS.

New functionality is added to the LAMMPS molecular simulation package, which increases the versatility with which LAMMPS can interface with supporting software and manipulate information associated with bonded force fields. We introduce the "type label" framework that allows atom types and their higher-order interactions (bonds, angles, dihedrals, and impropers) to be represented in terms of the standard atom type strings of a bonded force field. Type labels increase the human readability of input files, enable bonded force fields to be supported by the OpenKIM repository, simplify the creation of reaction templates for the REACTER protocol, and increase compatibility with external visualization tools, such as VMD and OVITO. An introductory primer on the forms and use of bonded force fields is provided to motivate this new functionality and serve as an entry point for LAMMPS and OpenKIM users unfamiliar with bonded force fields. The type label framework has the potential to streamline modeling workflows that use LAMMPS by increasing the portability of software, files, and scripts for preprocessing, running, and postprocessing a molecular simulation.

Assign_v2: a novel bonded-force field parameterization software for square planar palladium molecular dynamics simulations

In the present study, a requisite bonded force field for conducting molecular dynamics simulations of palladium compounds was derived utilizing a novel technique termed the “numbering system,” implemented through a program named assign.py. A significant challenge in deriving a bonded force field for square-planar palladium compounds emanates from their cis-trans characteristics, whereby the bond angles of identical atoms diverge across different compounds due to the presence of cis and trans isomers. To navigate this challenge, atoms surrounding the palladium were assigned numerical identifiers; consecutively numbered neighboring atoms were designated as “cis,” while atoms alternately numbered were regarded as “trans” relative to each other. Through the employment of the newly developed assign.py program, atoms common to GAFF were automatically assigned, facilitating the seamless integration of GAFF with the newly derived force field for cis and trans configurations. The tested innovative force field demonstrated results in close proximity to experimental findings. This research introduced two novel elements: firstly, a comparatively extensive force field was derived for palladium compounds, enabling the simulation of the previously non-simulable square planar geometry of palladium. Secondly, new software, assign.py, was developed, capable of amalgamating “numbering system atom types” with GAFF atom types into a unified force field. Conclusive tests within the study affirmed that the innovative bonded force field and technique utilizing the assign.py program was successful, simulating the square-planar geometry of palladium in a manner highly congruent with the experimental geometry. The program, licensed under Apache2, can be accessed via the following link: https://github.com/bkurt00/palladiumFF2/blob/main/assign_v2/assign_v2.py Communicated by Ramaswamy H. Sarma

Alternative Local Melting‐Solidification of Suspended Nanoparticles for Heterostructure Formation Enabled by Pulsed Laser Irradiation

AbstractPhase formation by pulsed laser irradiation of suspended nanoparticles has recently been introduced as a promising synthesis technique for heterostructures. The main challenge still lingers regarding the exact mechanism of particle formation due to the non‐equilibrium kinetic by‐products resulting from the localized alternative, fast, high‐temperature nature of the process. Here, the authors analyze the bond breaking/formation of copper or copper (II) interfaces with ethanol during the absorption of pulses for Cu‐CuO‐Cu2O formation applicable as an electrocatalyst in ethanol oxidation fuel cells. This study includes but is not limited to, a comprehensive discussion of the interaction between nano‐laser pulses and suspension for practical control of the synthesis process. The observed exponential and logarithmic changes in the content of heterostructures for the CuO‐ethanol and Cu‐ethanol samples irradiated with different fluences are interpreted as the dominant role of physical and chemical reactions, respectively, during the pulsed laser irradiation of suspensions synthesis. It is also shown that the local interface between dissociated ethanol and the molten sphere is responsible for the oxidative/reductive interactions resulting in the formation of catalytic‐augmented Cu3+ by‐product, thanks to the reactive bond force field molecular dynamics studies confirmed by ab‐initio calculations and experimental observations.

Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.

Advances in molecular dynamics (MD) software alongside enhanced computational power and hardware have allowed for MD simulations to significantly expand our knowledge of biomolecular structure, dynamics, and interactions. Furthermore, it has allowed for the extension of conformational sampling times from nanoseconds to the microsecond level and beyond. This has not only made convergence of conformational ensembles through comprehensive sampling possible but consequently exposed deficiencies and allowed the community to overcome limitations in the available force fields. The reproducibility and accuracy of the force fields are imperative in order to produce biologically relevant data. The Amber nucleic acid force fields have been used widely since the mid-1980s, and improvement of these force fields has been a community effort with several artifacts revealed, corrected, and reevaluated by various research groups. Here, we focus on the Amber force fields for use with double-stranded DNA and present the assessment of two recently developed force field parameter sets (OL21 and Tumuc1). Extensive MD simulations were performed with six test systems and two different water models. We observe the improvement of OL21 and Tumuc1 compared to previous generations of the Amber DNA force. We did not detect any significant improvement in the performance of Tumuc1 compared to OL21 despite the reparameterization of bonded force field terms in the former; however, we did note discrepancies in Tumuc1 when modeling Z-DNA sequences.

Coarse-Grained Dynamically Accurate Simulations of Ionic Liquids: [pyr14][TFSI] and [EMIM][BF4

In this work, coarse-grained (CG) models for two different sets of ionic liquids were developed from atomistic molecular dynamics (MD) reference systems, expanding their system size and time duration capabilities. The bonded force field of the CG systems was built using harmonic oscillator potential (HOP) fitting, while the nonbonded force field was generated with the multiscale coarse-graining (MS-CG) approach based on force matching. The dynamics of each system were corrected using the probability distribution function-based coarse-grained molecular dynamics (PDF-based CGMD) method. The structure and dynamics of each system were proven to match reference system data at two temperature scales. CG models and force fields for these liquids were developed to exemplify a general purpose methodology for producing MD results of ionic liquids and other fluids with accurate structural as well as dynamic properties. As an application, developed ionic liquids CG models were then applied to study vacuum-interface interaction. Density profile results of vacuum-interface exposure show significant deviation from bulk behavior. At the interface, multilayer ordering of ionic liquids is predicted to be similar to those observed from an experimental work. This ordering is intensified by decreasing temperature and use of the PDF-based CGMD method as opposed to conventional CG methods.

Discrete element modeling on crack evolution behavior of sandstone containing two oval flaws under uniaxial compression

To understand the fracture coalescence in specimens containing oval flaws, PFC2D was used to investigate the sandstone containing two oval flaws with different ligament angles under uniaxial compression. The micro-parameters were first confirmed by intact sandstone, and then, these were adopted to simulate the flawed specimen under uniaxial compression. Numerical results show that the peak strength, the peak strain, elastic modulus, and the ultimate failure modes were approximated well with these obtained by experiment. The failure modes obtained by numerical simulation can be divided into the following four typical categories based on the crack coalescence between the pre-existing flaws: no crack coalescence; indirect crack coalescence outside the bridge area; single crack coalescence inside the bridge area; tensile crack coalescence outside the bridge area. Based on parallel bond force fields and stress variation of measurement circles along the crack trajectory, the crack evolution processes were analyzed in detail and crack types were identified. The mode III can be divided into mode IIIa and mode IIIb. The mode IIIa is the single shear crack coalesced inside the bridge area; the mode IIIb is the single crack that initiated with tensile crack and coalesced with shear crack, and it only occurred as β = 90°. The mode IV can be divided into mode IVa and mode IVb. The mode IVa is that wing crack initiated at the middle of oval and coalesced at another oval tip, and it occurred as β = 120°. The mode IVb is that coalesced with anti-wing crack outside the bridge area, and it occurred as β = 150°. The stress distribution along the ligament has an obvious effect on ligament angle and flaw angle, and crack initiation only affects the stress concentration factor value.

Hybrid Molecular Dynamics for Elucidating Cooperativity Between Halogen Bond and Water Molecules During the Interaction of p53-Y220C and the PhiKan5196 Complex.

The cooperativity between hydrogen and halogen bonds plays an important role in rational drug design. However, mimicking the dynamic cooperation between these bonds is a challenging issue, which has impeded the development of the halogen bond force field. In this study, the Y220C–PhiKan5196 complex of p53 protein was adopted as a model, and the functions of three water molecules that formed hydrogen bonds with halogen atoms were analyzed by the simulation method governed by the hybrid quantum mechanical/molecular mechanical molecular dynamics. A comparison with the water-free model revealed that the strength of the halogen bond in the complex was consistently stronger. This confirmed that the water molecules formed weak hydrogen bonds with the halogen atom and cooperated with the halogen atom to enhance the halogen bond. Further, it was discovered that the roles of the three water molecules were not the same. Therefore, the results obtained herein can facilitate a rational drug design. Further, this work emphasizes on the fact that, in addition to protein pockets and ligands, the role of voids should also be considered with regard to the water molecules surrounding them.

Discrete Element Modeling of Strength and Failure Behavior of Transversely Isotropic Rock under Uniaxial Compression

Abstract This paper presents a discrete element modeling (DEM) with particle flow code 2D (PFC2D) for simulating the mechanical behavior of artificial transversely isotropic rock under uniaxial compression. The DEM model is established with the approach of synthetic rock mass (SRM) modeling, i.e. embedding joints of weak plane to the bonded particle model (BPM) of intact rock for simulating the joint rock. Sensitivity of joint micro-parameters is analyzed to provide references for calibrating micro-parameters of artificial transversely isotropic rock in PFC2D. The uniaxial compression test of DEM model displays U-shape variation of uniaxial compressive strength (UCS) along with bedding angle which is same to that of artificial transversely isotropic rock, a non-ignorable diversity in UCS value compared with the artificial transversely isotropic rock is also presented, while the normalized values of them are of well-matching. The obtained information of type, counts and distribution of micro-crack in PFC2D after DEM model failure indicate a remarkable impact on failure behavior of transversely isotropic rock, which cannot be surveyed in laboratory test. Farther more, the bond force field and particle displacement field reveal that separation zones caused by tension arise at bedding angle below 45°, while the shear zone occurs at bedding angle above 45°.

Automatic Assignment of Bonded Force Field Parameters for Small Molecules Using Machine Learning

Automatic Assignment of Bonded Force Field Parameters for Small Molecules Using Machine Learning

Investigating detailed mechanism of hydrogen molecules adsorbing on single-wall carbon nanotubes using fitted force field parameters containing carbon-carbon interactions.

The nonbonded and bonded force field parameters for carbon atoms in single-wall carbon nanotubes (SWNT) are fitted by means of quantum chemistry calculations with considering the periodic boundary conditions. The nonbonded parameters between carbon atoms and hydrogen atoms are fitted as well. All the fitted parameters are verified by comparing to quantum chemistry results and by calculating Young's modulus. Adsorption of Hydrogen molecules are then carried out on a bundle of self-assembled SWNTs. The adsorption isotherms are consistent to the Freundlich equation. Both hydrogen molecules adsorbed outside and inside the SWNTs are counted. According to our result, hydrogen molecules adsorbed inside the SWNTs are more stable at a relatively high temperature and are playing an important part in total amount of the adsorbed molecules. While C(10,10) have the highest adsorption capacities in most of the temperatures, hydrogen molecules inside C(5,5) are the most stable of all the four kinds of SWNTs. Thus, balancing adsorption capacities and strength of interaction can be important in choosing SWNT for gas adsorption. Besides, we deduct an equation that can describe the relation between hydrogen pressure and amount of SWNTs based on our simulation results. The hydrogen pressure may decrease by adding SWNTs in the system. The fitting method in our system is valid to SWNTs and can be tested in further studies of similar systems. © 2018 Wiley Periodicals, Inc.

Computational Study of PCSK9-EGFA Complex with Effective Polarizable Bond Force Field.

Inhibiting of Proprotein Convertase Subtilisin/Kexin-type 9 (PCSK9) and Low Density Lipoprotein Receptor (LDLR) binding is an effective way for reducing Low Density Lipoprotein cholesterol (LDL-C). Understanding the interaction between PCSK9 and LDLR is useful for PCSK9 inhibitor design. In this work, MD simulations with the standard (non-polarizable) AMBER force field and effective polarizable bond (EPB) force field were performed for wild type and four mutants of PCSK9 and EGFA (Epidermal Growth Factor-like repeat A) domain of LDLR complexes. These four mutants are gain-of-function mutants. The analysis of hydrogen bond dynamics and the relative binding free energy indicates that EPB is more reliable in simulating protein dynamics and predicting relative binding affinity. Structures sampled from MD simulations with the standard AMBER force field deviate too far away from crystal structures. Many important interaction components between of PCSK9 and EGFA no longer exist in the simulation with the Amber force field. For comparison, simulation using EPB force field gives more stable structures as shown by hydrogen bond analysis and produced relative binding free energies that are consistent with experimental results. Our study suggests that inclusion of polarization effects in MD simulation is important for studying the protein-protein interaction.

Harmonic Force Constants for Molecular Mechanics Force Fields via Hessian Matrix Projection.

A modification to the Seminario method [ Int. J. Quantum Chem. 1996 , 60 , 1271 - 1277 ] is proposed, which derives accurate harmonic bond and angle molecular mechanics force field parameters directly from the quantum mechanical Hessian matrix. The new method reduces the average error in the reproduction of quantum mechanical normal-mode frequencies of a benchmark set of 70 molecules from 12.3% using the original method, to 6.3%. The modified Seminario method is fully automated, and all parameters are computed directly from quantum mechanical data, thereby avoiding interdependency between bond and angle parameters and other components of the force field. A complete set of bond and angle force field parameters for the 20 naturally occurring amino acids is also provided for use in the future development of protein force fields.

Experimental and numerical study on the fracture coalescence behavior of rock-like materials containing two non-coplanar filled fissures under uniaxial compression

In this research, experimental and numerical simulations were adopted to investigate the effects of ligament angle on compressive strength and failure mode of rock-like material specimens containing two non-coplanar filled fissures under uniaxial compression. The experimental results show that with the increase of ligament angle, the compressive strength decreases to a nadir at the ligament angle of <TEX>$60^{\circ}$</TEX>, before increasing to the maximum at the ligament angle of <TEX>$120^{\circ}$</TEX>, while the elastic modulus is not obviously related to the ligament angle. The shear coalescence type easily occurred when <TEX>${\alpha}$</TEX> < <TEX>${\beta}$</TEX>, although having the same degree difference between the angle of ligament and fissure. Numerical simulations using <TEX>$PFC^{2D}$</TEX> were performed for flawed specimens under uniaxial compression, and the results are in good consistency with the experimental results. By analyzing the crack evolution process and parallel bond force field of rock-like material specimen containing two non-coplanar filled fissures, we can conclude that the coalescence and propagation of crack are mainly derived from parallel bond force, and the crack initiation and propagation also affect the distribution of parallel bond force. Finally, the displacement vectors in ligament region were used to identify the type of coalescence, and the results coincided with that obtained by analyzing parallel bond force field. These experimental and numerical results are expected to improve the understanding of the mechanism of flawed rock engineering structures.

Direct folding simulation of helical proteins using an effective polarizable bond force field.

We report a direct folding study of seven helical proteins (, Trpcage, , C34, N36, , ) ranging from 17 to 53 amino acids through standard molecular dynamics simulations using a recently developed polarizable force field-Effective Polarizable Bond (EPB) method. The backbone RMSDs, radius of gyrations, native contacts and native helix content are in good agreement with the experimental results. Cluster analysis has also verified that these folded structures with the highest population are in good agreement with their corresponding native structures for these proteins. In addition, the free energy landscape of seven proteins in the two dimensional space comprised of RMSD and radius of gyration proved that these folded structures are indeed of the lowest energy conformations. However, when the corresponding simulations were performed using the standard (nonpolarizable) AMBER force fields, no stable folded structures were observed for these proteins. Comparison of the simulation results based on a polarizable EPB force field and a nonpolarizable AMBER force field clearly demonstrates the importance of polarization in the folding of stable helical structures.

Strong scaling of general-purpose molecular dynamics simulations on GPUs

We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, 2013). Our approach is inspired by a traditional CPU-based code, LAMMPS (Plimpton, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., 2008). The software supports short-ranged pair force and bond force fields and achieves optimal GPU performance using an autotuning algorithm. We are able to demonstrate equivalent or superior scaling on up to 3375 GPUs in Lennard-Jones and dissipative particle dynamics (DPD) simulations of up to 108 million particles. GPUDirect RDMA capabilities in recent GPU generations provide better performance in full double precision calculations. For a representative polymer physics application, HOOMD-blue 1.0 provides an effective GPU vs. CPU node speed-up of 12.5×.

Toward the development of the potential with angular distortion for halogen bond: a comparison of potential energy surfaces between halogen bond and hydrogen bond.

As noncovalent intermolecular interactions, hydrogen bond (HB) and halogen bond (XB) are attracting increasing attention. In this work, the potential energy surfaces (PESs) of hydrogen and halogen bonds are compared. Twelve halogen-bonded and three hydrogen-bonded models are scanned for analysis using the MP2 level of theory. This work indicates that potential energy surfaces of both HB and XB have angular distortion. The potential well of XB is narrower than that of HB. With the elongation of the bond length, the potential energy surfaces get flatter. The best fitting functions for angular distortion and the flattening character of angular terms are also combined into a modified Buckingham potential. The testing results show that the essential features of the PES, including angular distortion and flattening character, have been reproduced. These results provide a better understanding of halogen and hydrogen bonds and the optimization of halogen bond force fields.

Friction Coefficient Calculation and Mechanism Analysis for MoS2 Nanoparticle from Molecular Dynamics Simulation

We studied friction coefficients and mechanisms of MoS2 nanoparticles from molecular dynamics simulations. A covalent bond force field of molybdenum and sulfur were implemented in LAMMPS and tri-layered capsular structured MoS2 nanoparticles subjected to different amplitudes of normal stress were performed. We found average friction coefficient predicted by molecular dynamics simulations is about 0.05, agreed well with experimental measurements. In addition, when the underlying mechanisms switched from sliding to rolling, significant reduction of friction coefficients was observed.

Protein Backbone Dynamics Simulations Using Coarse-Grained Bonded Potentials and Simplified Hydrogen Bonds.

A new set of bonded potentials is introduced to model the flexibility of coarse-grained polypeptide chains. Based on a statistical analysis of known structures, the bonded potentials are sequence-dependent, and the secondary-structure propensity of each amino acid is partially reflected in the Si-Bi-Bi+1-Bi+2 pseudotorsion angle, where Si and Bi denote the side-chain and backbone beads, respectively. To stabilize the secondary structures during simulations, the bonded force field must be balanced by a simplified model of the protein hydrogen bonds, based on dipole-dipole interactions. Tested on eight polypeptides with sequence lengths ranging from 17 to 98, using 200-ns molecular dynamics simulations, the coarse-grained model yields trajectories with RMSDs ranging from 3 to 8 Å from the experimental conformations. The less-structured regions of the simulated proteins exhibit the largest-amplitude movements.

Photostability via Sloped Conical Intersections: A Computational Study of the Pyrene Radical Cation

The photophysics of the pyrene radical cation, a polycyclic aromatic hydrocarbon (PAH) and a possible source of diffuse interstellar bands (DIBs), is investigated by means of hybrid molecular mechanics-valence bond (MMVB) force field and multiconfigurational CASSCF and CASPT2 ab initio methods. Potential energy surfaces of the first three electronic states D 0, D 1, and D 2 are calculated. MMVB geometry optimizations are carried out for the first time on a cationic system; the results show good agreement with CASSCF optimized structures, for minima and conical intersections, and errors in the energy gaps are no larger than those found in our previous studies of neutral systems. The presence of two easily accessible sloped D 1/D 2 and D 0/D 1 conical intersections suggests the pyrene radical cation is highly photostable, with ultrafast nonradiative decay back to the initial ground state geometry predicted via a mechanism similar to the one found in the naphthalene radical cation.

Molecular dynamics study of the ionic conductivity of 1-n-butyl-3-methylimidazolium salts as ionic liquids

Abstract We have performed a molecular dynamics simulation to investigate the ionic conductivities of the 1-n-butyl-3-methylimidazolium salts [BMIM]+[Anion]− as ionic liquids, where the anions are PF 6 - and the fluorinated organic anions CF3COO−, C3F7COO−, CF 3 SO 3 - , and C 4 F 9 SO 3 - . We developed bonded force field parameters for the anions and applied them to the molecular dynamics simulations. The calculated ionic conductivities are qualitatively in good agreement with the experimental values, demonstrating that the volume and self-diffusion coefficient of ionic liquids are important factors in determining the ionic conductivity of ionic liquids.