Search results for "force field"
showing 10 items of 55 documents
Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.
2010
Coarse-grained molecular dynamics simulations offer a dramatic extension of the time-scale of simulations compared to all-atom approaches. In this article, we describe the use of the physics-based united-residue (UNRES) force field, developed in our laboratory, in protein-structure simulations. We demonstrate that this force field offers about a 4000-times extension of the simulation time scale; this feature arises both from averaging out the fast-moving degrees of freedom and reduction of the cost of energy and force calculations compared to all-atom approaches with explicit solvent. With massively parallel computers, microsecond folding simulation times of proteins containing about 1000 r…
Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics
2021
Apart from being the most common mechanism of regulating protein function and transmitting signals throughout the cell, phosphorylation has an ability to induce disorder-to-order transition in an intrinsically disordered protein. In particular, it was shown that folding of the intrinsically disordered protein, eIF4E-binding protein isoform 2 (4E-BP2), can be induced by multisite phosphorylation. Here, the principles that govern the folding of phosphorylated 4E-BP2 (pT37pT46 4E-BP2(18–62)) are investigated by analyzing canonical and replica exchange molecular dynamics trajectories, generated with the coarse-grained united-residue force field, in terms of local and global motions and the time…
Coarse Graining of Short Polythylene Chains for Studying Polymer Crystallization.
2015
We derive coarse-grained models of polyethylene in the melt state with the aim to study polymer crystallization. This requires a low level of coarse-graining: We use a mapping of two CH2 groups onto one bead. The coarse-grained beads are connected with harmonic springs, an optimized angular potential, and an optional torsional potential. Coarse-grained potentials are derived from detailed all-atom simulations, and an optimized form of the force field is then derived which achieves a good accuracy in reproducing the static properties of the chains. We address the question over which temperature range such models can be used, and in particular if the model is capable of reproducing the phase…
Optimization of Reactive Force Field Simulation: Refactor, Parallelization, and Vectorization for Interactions
2022
Molecular dynamics (MD) simulations are playing an increasingly important role in many areas ranging from chemical materials to biological molecules. With the continuing development of MD models, the potentials are getting larger and more complex. In this article, we focus on the reactive force field (ReaxFF) potential from LAMMPS to optimize the computation of interactions. We present our efforts on refactoring for neighbor list building, bond order computation, as well as valence angles and torsion angles computation. After redesigning these kernels, we develop a vectorized implementation for non-bonded interactions, which is nearly $100 \times$ 100 × faster than the management processing…
Global stability of protein folding from an empirical free energy function
2013
The principles governing protein folding stand as one of the biggest challenges of Biophysics. Modeling the global stability of proteins and predicting their tertiary structure are hard tasks, due in part to the variety and large number of forces involved and the difficulties to describe them with sufficient accuracy. We have developed a fast, physics-based empirical potential, intended to be used in global structure prediction methods. This model considers four main contributions: Two entropic factors, the hydrophobic effect and configurational entropy, and two terms resulting from a decomposition of close-packing interactions, namely the balance of the dispersive interactions of folded an…
Iron’s Wake: The Performance of Quantum Mechanical-Derived Versus General-Purpose Force Fields Tested on a Luminescent Iron Complex
2020
Recently synthetized iron complexes have achieved long-lived excited states and stabilities which are comparable, or even superior, to their ruthenium analogues, thus representing an eco-friendly and cheaper alternative to those materials based on rare metals. Most of computational tools which could help unravel the origin of this large efficiency rely on ab-initio methods which are not able, however, to capture the nanosecond time scale underlying these photophysical processes and the influence of their realistic environment. Therefore, it exists an urgent need of developing new low-cost, but still accurate enough, computational methodologies capable to deal with the steady-state and trans…
The Use of X-ray Absorption Spectra for Validation of Classical Force-Field Models
2015
Abstract Extended X-ray absorption fine structure (EXAFS) spectroscopy and molecular dynamics (MD) simulations are two complementary techniques widely used to study the atomic structure of materials. Their combined use, known as the MD-EXAFS approach, allows one to access the structural information, encoded in EXAFS, far beyond the nearest coordination shells and to validate the accuracy of the interaction potential models. In this study we demonstrate the use of the MD-EXAFS method for a validation of several force-field models on an example of the cubic-perovskite SrTiO3 and hexagonal wurtzite-type ZnO crystals.
Local vs global motions in protein folding
2013
It is of interest to know whether local fluctuations in a polypeptide chain play any role in the mechanism by which the chain folds to the native structure of a protein. This question is addressed by analyzing folding and non-folding trajectories of a protein; as an example, the analysis is applied to the 37-residue triple β-strand WW domain from the Formin binding protein 28 (FBP28) (PDB ID: 1E0L). Molecular dynamics (MD) trajectories were generated with the coarse-grained united-residue force field, and one- and two-dimensional free-energy landscapes (FELs) along the backbone virtual-bond angle θ and backbone virtual-bond-dihedral angle γ of each residue, and principal components, respect…
An Accurate Quartic Force Field and Fundamental Frequencies for the Ozonide Anion: A Rare Positive Anharmonicity for the Antisymmetric Stretch
2003
The CCSD(T) method has been used to compute a highly accurate quartic force field and fundamental frequencies for all 16O and 18O isotopomers of the ozonide anion. The CCSD and CASPT2 methods have also been used to verify the reliability of the CCSD(T) fundamental frequencies. The computed fundamental frequencies are in agreement with gas-phase experiments, but disagree with matrix isolation experiments for the antisymmetric stretch, ν3. CASPT2 calculations show that the antisymmetric part of the O3- potential surface is sensitive to the external environment. It is concluded that the antisymmetric stretch exhibits a significant matrix shift in the matrix isolation experiments and that the m…
Molecular mechanics models for the image charge, a comment on “including image charge effects in the molecular dynamics simulations of molecules on m…
2017
We re-investigate the image charge model of Iori and Corni (Iori and Corni, J. Comput. Chem. 2008, 29, 1656). We find that a simple symmetrization of their model allows to obtain quantitatively correct results for the electrostatic interaction of a water molecule with a metallic surface. This symmetrization reduces the magnitude of the electrostatic interaction to less than 10% of the total interaction energy. © 2017 Wiley Periodicals, Inc.