Molecular Dynamics Simulation Package Research Articles

Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles.

Far from the static, idealized conformations deposited into structural databases, proteins are highly dynamic molecules that undergo conformational changes on temporal and spatial scales that may span several orders of magnitude. These conformational changes, often intimately connected to the functional roles that proteins play, may be obscured by traditional biophysical techniques. Over the past 40 years, molecular dynamics (MD) simulations have complemented these techniques by providing the "hidden" atomistic details that underlie protein dynamics. However, there are limitations of the degree to which molecular simulations accurately and quantitatively describe protein motions. Here we show that although four molecular dynamics simulation packages (AMBER, GROMACS, NAMD, and ilmm) reproduced a variety of experimental observables for two different proteins (engrailed homeodomain and RNase H) equally well overall at room temperature, there were subtle differences in the underlying conformational distributions and the extent of conformational sampling obtained. This leads to ambiguity about which results are correct, as experiment cannot always provide the necessary detailed information to distinguish between the underlying conformational ensembles. However, the results with different packages diverged more when considering larger amplitude motion, for example, the thermal unfolding process and conformational states sampled, with some packages failing to allow the protein to unfold at high temperature or providing results at odds with experiment. While most differences between MD simulations performed with different packages are attributed to the force fields themselves, there are many other factors that influence the outcome, including the water model, algorithms that constrain motion, how atomic interactions are handled, and the simulation ensemble employed. Here four different MD packages were tested each using best practices as established by the developers, utilizing three different protein force fields and three different water models. Differences between the simulated protein behavior using two different packages but the same force field, as well as two different packages with different force fields but the same water models and approaches to restraining motion, show how other factors can influence the behavior, and it is incorrect to place all the blame for deviations and errors on force fields or to expect improvements in force fields alone to solve such problems.

GRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.

Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residue-residue interaction energies from user-supplied simulation trajectories, greatly simplifying the analysis for the end-user. A GUI, including an embedded molecular viewer, is provided for visualization of interaction energy time-series, distributions, an interaction energy matrix, interaction energy correlations and a residue correlation matrix. gRINN additionally offers construction and analysis of Protein Energy Networks, providing residue-based metrics such as degrees, betweenness-centralities, closeness centralities as well as shortest path analysis. gRINN is free and open to all users without login requirement at http://grinn.readthedocs.io.

Incremental update of electrostatic interactions in adaptively restrained particle simulations

The computation of long-range potentials is one of the demanding tasks in Molecular Dynamics. During the last decades, an inventive panoply of methods was developed to reduce the CPU time of this task. In this work, we propose a fast method dedicated to the computation of the electrostatic potential in adaptively restrained systems. We exploit the fact that, in such systems, only some particles are allowed to move at each timestep. We developed an incremental algorithm derived from a multigrid-based alternative to traditional Fourier-based methods. Our algorithm was implemented inside LAMMPS, a popular molecular dynamics simulation package. We evaluated the method on different systems. We showed that the new algorithm's computational complexity scales with the number of active particles in the simulated system, and is able to outperform the well-established Particle Particle Particle Mesh (P3M) for adaptively restrained simulations. © 2018 Wiley Periodicals, Inc.

DROIDS 1.20: A GUI-Based Pipeline for GPU-Accelerated Comparative Protein Dynamics

Traditional informatics in comparative genomics work only with static representations of biomolecules (i.e., sequence and structure), thereby ignoring the molecular dynamics (MD) of proteins that define function in the cell. A comparative approach applied to MD would connect this very short timescale process, defined in femtoseconds, to one of the longest in the universe: molecular evolution measured in millions of years. Here, we leverage advances in graphics-processing-unit-accelerated MD simulation software to develop a comparative method of MD analysis and visualization that can be applied to any two homologous Protein Data Bank structures. Our open-source pipeline, DROIDS (Detecting Relative Outlier Impacts in Dynamic Simulations), works in conjunction with existing molecular modeling software to convert any Linux gaming personal computer into a “comparative computational microscope” for observing the biophysical effects of mutations and other chemical changes in proteins. DROIDS implements structural alignment and Benjamini-Hochberg-corrected Kolmogorov-Smirnov statistics to compare nanosecond-scale atom bond fluctuations on the protein backbone, color mapping the significant differences identified in protein MD with single-amino-acid resolution. DROIDS is simple to use, incorporating graphical user interface control for Amber16 MD simulations, cpptraj analysis, and the final statistical and visual representations in R graphics and UCSF Chimera. We demonstrate that DROIDS can be utilized to visually investigate molecular evolution and disease-related functional changes in MD due to genetic mutation and epigenetic modification. DROIDS can also be used to potentially investigate binding interactions of pharmaceuticals, toxins, or other biomolecules in a functional evolutionary context as well.

Study on optical films with AgNWs using UV laser patterning

Silver nanowires (AgNWs) with excellent conductive properties can be used to make transparent electrodes with high transmittance, low haze, high electrical conductivity, and high mechanical strength. AgNWs could be a promising material to replace indium tin oxide (ITO). In this study, a polyol method was used to synthesize one-dimension AgNWs. Molecular dynamics simulation software of the Large-scale Atomic/Molecular Massively Parallel Simulator was applied to analyze the micro/nano-scale behavior and predict basic mechanical properties of the materials. For optical properties, a near-field electrospray was combined with ultraviolet 355-nm laser ablation process to direct-write patterning of the transparent conductive AgNWs films as electrodes. Three conductive films with various thicknesses of AgNWs prepared by the near-field electrospray process were coated on glass substrates to analyze the surface morphology and optical properties. A scanning electron microscope and energy dispersive spectrometer were utilized to observe the surface morphology and material composition. An optical integrating sphere and a four-point probe were used to examine the transmittance, haze, and electrical conductivity, respectively. In this study, the optical, electrical and mechanical characteristic as a function of thickness of the films, and laser power levels were characterized.

DL_ANALYSER Notation for Atomic Interactions (DANAI): A Natural Annotation System for Molecular Interactions, Using Ethanoic Acid Liquid as a Test Case.

The DL_ANALYSER Notation for Atomic Interactions, DANAI, is the notation syntax to describe interactions between molecules. This notation can annotate precisely the detailed atomistic interactions without having to resolve to diagrammatic illustrations, and yet can be interpreted easily by both human users and computational means. By making use of the DL_F Notation, a universal atom typing scheme for molecular simulations, DANAI contains the expression of atomic species in a natural chemical sense. It is implemented within DL_ANALYSER, a general analysis software program for DL_POLY molecular dynamics simulation software. By making references to the molecular dynamics simulations of pure ethanoic acid liquid, it is shown that DL_ANALYSER can identify and distinguish a variety of hydrogen bond and hydrophobic contact networks through the use of the DANAI expression. It was found that the carboxylic groups preferentially orientated in a “head-to-tail” conformation to form hydrogen bonds between the carbonyl oxygen and hydroxyl hydrogen, resulting in a series of linear structures that intertwined with pockets of methyl clusters.

RUMD: A general purpose molecular dynamics package optimized to utilize GPU hardware down to a few thousand particles

RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU’s). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating small to medium system sizes (roughly from a few thousand up to hundred thousand particles). It has a performance that is comparable to other GPU-MD codes at large system sizes and substantially better at smaller sizes. RUMD is open-source and consists of a library written in C++ and the CUDA extension to C, an easy-to-use Python interface, and a set of tools for set-up and post-simulation data analysis. The paper describes RUMD’s main features, optimizations and performance benchmarks.

Increasing vaccine production using pulsed ultrasound waves.

Vaccination is a safe and effective approach to prevent deadly diseases. To increase vaccine production, we propose that a mechanical stimulation can enhance protein production. In order to prove this hypothesis, Sf9 insect cells were used to evaluate the increase in the expression of a fusion protein from hepatitis B virus (HBV S1/S2). We discovered that the ultrasound stimulation at a frequency of 1.5 MHz, intensity of 60 mW/cm2, for a duration of 10 minutes per day increased HBV S1/S2 by 27%. We further derived a model for transport through a cell membrane under the effect of ultrasound waves, tested the key assumptions of the model through a molecular dynamics simulation package, NAMD (Nanoscale Molecular Dynamics program) and utilized CHARMM force field in a steered molecular dynamics environment. The results show that ultrasound waves can increase cell permeability, which, in turn, can enhance nutrient / waste exchange thus leading to enhanced vaccine production. This finding is very meaningful in either shortening vaccine production time, or increasing the yield of proteins for use as vaccines.

Molecular-dynamic simulations of the thermophysical properties of hexanitrohexaazaisowurtzitane single crystal at high pressures and temperatures

Molecular dynamic simulations of isothermal compression parameters are performed for a hexanitrohexaazaisowurtzitane single crystal (C6H6O12N12) using a modified ReaxFF-log reactive force field. It is shown that the pressure–compression ratio curve for a single C6H6O12N12 crystal at constant temperature T = 300 K in pressure range P = 0.05–40 GPa is in satisfactory agreement with experimental compression isotherms obtained for a single C6H6O12N12 crystal. Hugoniot molecular-dynamic simulations of the shock-wave hydrostatic compression of a single C6H6O12N12 crystal are performed. Along with Hugoniot temperature–pressure curves, calculated shock-wave pressure–compression ratios for a single C6H6O12N12 crystal are obtained for a wide pressure range of P = 1–40 GPa. It is established that the percussive adiabat obtained for a single C6H6O12N12 crystal is in a good agreement with the experimental data. All calculations are performed using a LAMMPS molecular dynamics simulation software package that provides a ReaxFF-lg reactive force field to support the approach.

Interfacial Bonding Energy on the Interface between ZChSnSb/Sn Alloy Layer and Steel Body at Microscale.

To investigate the performance of bonding on the interface between ZChSnSb/Sn and steel body, the interfacial bonding energy on the interface of a ZChSnSb/Sn alloy layer and the steel body with or without Sn as an intermediate layer was calculated under the same loadcase using the molecular dynamics simulation software Materials Studio by ACCELRYS, and the interfacial bonding energy under different Babbitt thicknesses was compared. The results show that the bonding energy of the interface with Sn as an intermediate layer is 10% larger than that of the interface without a Sn layer. The interfacial bonding performances of Babbitt and the steel body with Sn as an intermediate layer are better than those of an interface without a Sn layer. When the thickness of the Babbitt layer of bushing is 17.143 Å, the interfacial bonding energy reaches the maximum, and the interfacial bonding performance is optimum. These findings illustrate the bonding mechanism of the interfacial structure from the molecular level so as to ensure the good bonding properties of the interface, which provides a reference for the improvement of the bush manufacturing process from the microscopic point of view.

Atomistic Corrective Scheme for Supercell Density Functional Theory Calculations of Charged Defects

A new method to correct formation energies of charged defects obtained by supercell density-functional calculations is presented and applied to bulk, surface, and low-dimensional systems. The method relies on atomistic models and a polarizable force field to describe a material system and its dielectric properties. The polarizable force field is based on a minimal set of fitting parameters, it accounts for the dielectric screening arising from ions and electrons separately, and it can be easily implemented in any software for atomistic molecular dynamics simulations. This work illustrates both technical aspects and applications of the new corrective scheme. The method is tested on systems in vacuo to validate the energy scheme. It is applied to charged defects in the bulk and at the surface of realistic materials to achieve comparison with published results obtained by using available corrective schemes based on continuum electrostatics treatments. Moreover, to demonstrate its generality, the method is used to correct the formation energy obtained by DFT of a singly negatively charged S vacancy in monolayer, bilayer, trilayer and bulk MoS2.

Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.

Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.

Getting the Right Answers for the Right Reasons: Toward Predictive Molecular Simulations of Water with Many-Body Potential Energy Functions.

The central role played by water in fundamental processes relevant to different disciplines, including chemistry, physics, biology, materials science, geology, and climate research, cannot be overemphasized. It is thus not surprising that, since the pioneering work by Stillinger and Rahman, many theoretical and computational studies have attempted to develop a microscopic description of the unique properties of water under different thermodynamic conditions. Consequently, numerous molecular models based on either molecular mechanics or ab initio approaches have been proposed over the years. However, despite continued progress, the correct prediction of the properties of water from small gas-phase clusters to the liquid phase and ice through a single molecular model remains challenging. To large extent, this is due to the difficulties encountered in the accurate modeling of the underlying hydrogen-bond network in which both number and strength of the hydrogen bonds vary continuously as a result of a subtle interplay between energetic, entropic, and nuclear quantum effects. In the past decade, the development of efficient algorithms for correlated electronic structure calculations of small molecular complexes, accompanied by tremendous progress in the analytical representation of multidimensional potential energy surfaces, opened the doors to the design of highly accurate potential energy functions built upon rigorous representations of the many-body expansion (MBE) of the interaction energies. This Account provides a critical overview of the performance of the MB-pol many-body potential energy function through a systematic analysis of energetic, structural, thermodynamic, and dynamical properties as well as of vibrational spectra of water from the gas to the condensed phase. It is shown that MB-pol achieves unprecedented accuracy across all phases of water through a quantitative description of each individual term of the MBE, with a physically correct representation of both short- and long-range many-body contributions. Comparisons with experimental data probing different regions of the water potential energy surface from clusters to bulk demonstrate that MB-pol represents a major step toward the long-sought-after "universal model" capable of accurately describing the molecular properties of water under different conditions and in different environments. Along this path, future challenges include the extension of the many-body scheme adopted by MB-pol to the description of generic solutes as well as the integration of MB-pol in an efficient theoretical and computational framework to model acid-base reactions in aqueous environments. In this context, given the nontraditional form of the MB-pol energy and force expressions, synergistic efforts by theoretical/computational chemists/physicists and computer scientists will be critical for the development of high-performance software for many-body molecular dynamics simulations.

A new force field including charge directionality for TMAO in aqueous solution

We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (OTMAO) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around OTMAO to mimic the OTMAO lone pairs and we migrate the negative charge on the OTMAO to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasing TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.

Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations.

DL_F Notation is an easy-to-understand, standardized atom typesetting expression for molecular simulations for a range of organic force field (FF) schemes such as OPLSAA, PCFF, and CVFF. It is implemented within DL_FIELD, a software program that facilitates the setting up of molecular FF models for DL_POLY molecular dynamics simulation software. By making use of the Notation, a single core conversion module (the DL_F conversion Engine) implemented within DL_FIELD can be used to analyze a molecular structure and determine the types of atoms for a given FF scheme. Users only need to provide the molecular input structure in a simple xyz format and DL_FIELD can produce the necessary force field file for DL_POLY automatically. In commensurate with the development concept of DL_FIELD, which placed emphasis on robustness and user friendliness, the Engine provides a single-step solution to setup complex FF models. This allows users to switch from one of the above-mentioned FF seamlessly to another while at the same time provides a consistent atom typing that is expressed in a natural chemical sense.

Crystal MD: The massively parallel molecular dynamics software for metal with BCC structure

Material irradiation effect is one of the most important keys to use nuclear power. However, the lack of high-throughput irradiation facility and knowledge of evolution process, lead to little understanding of the addressed issues. With the help of high-performance computing, we could make a further understanding of micro-level-material. In this paper, a new data structure is proposed for the massively parallel simulation of the evolution of metal materials under irradiation environment. Based on the proposed data structure, we developed the new molecular dynamics software named Crystal MD. The simulation with Crystal MD achieved over 90% parallel efficiency in test cases, and it takes more than 25% less memory on multi-core clusters than LAMMPS and IMD, which are two popular molecular dynamics simulation software. Using Crystal MD, a two trillion particles simulation has been performed on Tianhe-2 cluster.

MCPB.py: A Python Based Metal Center Parameter Builder.

MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach. It has an optimized code structure, with far fewer required steps than the previous developed MCPB program. It supports various AMBER force fields and more than 80 metal ions. A series of parametrization schemes to derive force constants and charge parameters are available within the program. We give two examples (one metalloprotein example and one organometallic compound example), indicating the program's ability to build reliable force fields for different metal ion containing complexes. The original version was released with AmberTools15. It is provided via the GNU General Public License v3.0 (GNU_GPL_v3) agreement and is free to download and distribute. MCPB.py provides a bridge between quantum mechanical calculations and molecular dynamics simulation software packages thereby enabling the modeling of metal ion centers. It offers an entry into simulating metal ions in a number of situations by providing an efficient way for researchers to handle the vagaries and difficulties associated with metal ion modeling.

Determination of anharmonic free energy contributions: Low temperature phases of the Lennard-Jones system.

We investigate a general method to calculate the free energy of crystalline solids by considering the harmonic approximation and quasistatically switching the anharmonic contribution. The advantage of this method is that the harmonic approximation provides an already very accurate estimate of the free energy, and therefore the anharmonic term is numerically very small and can be determined to high accuracy. We further show that the anharmonic contribution to the free energy satisfies a number of exact inequalities that place constraints on its magnitude and allows approximate but fast and accurate estimates. The method is implemented into a readily available general software by combining the code HOODLT (Highly Optimized Object Oriented Dynamic Lattice Theory) for the harmonic part and the molecular dynamics (MD) simulation package HOOMD-blue for the anharmonic part. We use the method to calculate the low temperature phase diagram for Lennard-Jones particles. We demonstrate that hcp is the equilibrium phase at low temperature and pressure and obtain the coexistence curve with the fcc phase, which exhibits reentrant behavior. Several implications of the method are discussed.

Visualizing the Dynamics of Neuronal Signaling

If a picture is worth a thousand words, how many words can a movie replace?The most popular molecular visualization software for molecular dynamics (MD) simulations is optimal for doing just that, visualizing MD simulations. Since MD simulations are usually performed on a limited number of actors in an isolated system, visualizations created with these tools lack the cellular context that is critical to understanding the broader context for molecular interactions and signaling.Although it is possible to show entire cellular systems with corresponding molecular actors using professional 3D animation software, this software is not directly compatible with the output of MD simulation engines. Furthermore, the amount of data generated in an MD simulation is very large and requires processing for optimal use in animations.We are developing a workflow and software tools (Molecular Maya) for combining MD simulations with other types of experimental data in animations of molecular systems. Our goal is not only to enable more realistic depictions of molecular movement in animations, but also to allow researchers to gain more control over their data visualizations as well as the cellular context within which these are depicted.

Easy and Fast Setup of Molecular Dynamics Simulations: Combining VMD and NAMD for Experimentalists

The relationship between structure and function of proteins is directly connected to atomistic aspects of protein dynamics. As a major methodology in structural biology, molecular dynamics (MD) simulations permit the exploration of the physical mechanism underlying the function of proteins by examining their dynamical behavior. Although the advances in MD simulations are leading to a new level of knowledge of macromolecular complexes, reaching the million-to-billion atom regime (1), the vast majority of MD users are interested in straightforward MD simulations of relatively simple proteins. Particularly in the last few years, structural biology experimentalists’ interest in performing MD simulations to improve their knowledge of a protein structure/function relationship has increased greatly. To assist these experimentalists and any novice to MD to overcome the initial learning curve barrier of MD simulation software, we developed a user interface (plugin) that connects the widely employed and user-friendly molecular graphics program VMD to the widely adopted MD program NAMD. Employing this plugin, a user is able to setup an MD simulation in just a few minutes, allowing quick studies of point mutations, partial deletions and even atomic force microscopy experiments. The plugin makes it easy for a new user to perform MD simulations, while it also servers as a learning tool. Many “info buttons” provide the theoretical background underlying the MD procedures carried out in modern MD simulations.1. Perilla, J.R., et al. 2015. Molecular dynamics simulations of large macromolecular complexes. Curr. Opin. Struct. Biol. 31: 64-74.