A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed.     

An automated approach for the parameterization of accurate intermolecular force‐fields: Pyridine as a case study

An automated protocol is proposed and validated, which integrates accurate quantum mechanical calculations with classical numerical simulations. Intermolecular force fields, (FF) suitable for molecular dynamics (MD) and Monte Carlo simulations, are parameterized through a novel iterative approach, fully based on quantum mechanical data, which has been automated and coded into the PICKY software, here presented. The whole procedure is tested and validated for pyridine, whose bulk phase, described through MD simulations performed with the specifically parameterized FF, is characterized by computing several of its thermodynamic, structural, and transport properties, comparing them with their experimental counterparts. © 2011 Wiley Periodicals, Inc.     

MATCH: an atom-typing toolset for molecular mechanics force fields

We introduce a toolset of program libraries collectively titled multipurpose atom-typer for CHARMM (MATCH) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion of multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges, and force field parameters are achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In this work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond charge increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM general force field (Vanommeslaeghe, et al., J Comput Chem 2010, 31, 671), one million molecules from the PubChem database of small molecules are typed, parameterized, and minimized.     

Simultaneous identification of unknown time delays and model parameters in uncertain dynamical systems with linear or nonlinear parameterization by autosynchronization

In this paper, we propose a general method to simultaneously identify both unknown time delays and unknown model parameters in delayed dynamical systems based on the autosynchronization technique. The design procedure is presented in detail by constructing a specific Lyapunov function and linearizing the model function with nonlinear parameterization. The obtained result can be directly extended to the identification problem of linearly parameterized dynamical systems. Two Wpical numerical examples confirming the effectiveness of the identification method are given.     

Integrable KP Coupling and Its Exact Solution

The integrable coupling is one of the most important topics in the nonlinear physics. This paper creates a novel integrable KP coupling and solves it via a recently-developed dark parameterization procedure.     

A numerical solution of problems in calculus of variation using direct method and nonclassical parameterization

In this paper a direct method for solving variational problems using nonclassical parameterization is presented. A nonclassical parameterization based on nonclassical orthogonal polynomials is first introduced to reduce a variational problem to a nonlinear mathematical programming problem. Then, using the Lagrange multiplier technique the problem is converted to that of solving a system of algebraic equations. Illustrative examples are given to demonstrate the validity and applicability of the technique.     

Initial Decomposition Mechanism of 3-Nitro-1,2,4-triazol-5-one (NTO) under Shock Loading: ReaxFF Parameterization and Molecular Dynamic Study

We report a reactive molecular dynamic (ReaxFF-MD) study using the newly parameterized ReaxFF-lg reactive force field to explore the initial decomposition mechanism of 3-Nitro-1,2,4-triazol-5-one (NTO) under shock loading (shock velocity >6 km/s). The new ReaxFF-lg parameters were trained from massive quantum mechanics data and experimental values, especially including the bond dissociation curves, valence angle bending curves, dihedral angle torsion curves, and unimolecular decomposition paths of 3-Nitro-1,2,4-triazol-5-one (NTO), 1,3,5-Trinitro-1,3,5-triazine (RDX), and 1,1-Diamino-2,2-dinitroethylene (FOX-7). The simulation results were obtained by analyzing the ReaxFF dynamic trajectories, which predicted the most frequent chain reactions that occurred before NTO decomposition was the unimolecular NTO merged into clusters ((C₂H₂O₃N₄)_n). Then, the NTO dissociated from (C₂H₂O₃N₄)_n and started to decompose. In addition, the paths of NO₂ elimination and skeleton heterocycle cleavage were considered as the dominant initial decomposition mechanisms of NTO. A small amount of NTO dissociation was triggered by the intermolecular hydrogen transfer, instead of the intramolecular one. For α-NTO, the calculated equation of state was in excellent agreement with the experimental data. Moreover, the discontinuity slope of the shock-particle velocity equation was presented at a shock velocity of 4 km/s. However, the slope of the shock-particle velocity equation for β-NTO showed no discontinuity in the shock wave velocity range of 3–11 km/s. These studies showed that MD by using a suitable ReaxFF-lg parameter set, could provided detailed atomistic information to explain the shock-induced complex reaction mechanisms of energetic materials. With the ReaxFF-MD coupling MSST method and a cheap computational cost, one could also obtain the deformation behaviors and equation of states for energetic materials under conditions of extreme pressure.