Symmetry-adapted graph neural networks for constructing molecular dynamics force fields

نویسندگان

چکیده

Molecular dynamics is a powerful simulation tool to explore material properties. Most realistic systems are too large be simulated using first-principles molecular dynamics. Classical has lower computational cost but requires accurate force fields achieve chemical accuracy. In this work, we develop symmetry-adapted graph neural network framework called the (MDGNN) construct automatically for simulations both molecules and crystals. This architecture consistently preserves translation, rotation, permutation invariance in simulations. We also propose new feature engineering method that includes high-order terms of interatomic distances demonstrate MDGNN accurately reproduces results classical addition, constructed by proposed model have good transferability. The thus an efficient promising option performing large-scale with high

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Constructing ab initio force fields for molecular dynamics simulations

We explore and discuss several important issues concerning the derivation of many-body force fields from ab initio quantum chemical data. In particular, we seek a general methodology for constructing ab initio force fields that are ‘‘chemically accurate’’ and are computationally efficient for large-scale molecular dynamics simulations. We investigate two approaches for modeling many-body intera...

متن کامل

Force fields and molecular dynamics simulations

The objective of this review is to serve as an introductory guide for the non-expert to the exciting field of Molecular Dynamics (MD). MD simulations generate a phase space trajectory by integrating the classical equations of motion for a system of N particles. Here I review the basic concepts needed to understand the technique, what are the key elements to perform a simulation and which is the...

متن کامل

Representing molecule-surface interactions with symmetry-adapted neural networks.

The accurate description of molecule-surface interactions requires a detailed knowledge of the underlying potential-energy surface (PES). Recently, neural networks (NNs) have been shown to be an efficient technique to accurately interpolate the PES information provided for a set of molecular configurations, e.g., by first-principles calculations. Here, we further develop this approach by buildi...

متن کامل

Iterative Force-Field Calculation and Molecular Dynamics of Cyclooctanone

Body's iterative force-field computer program has been used to calculate strain energies in cyclooctanone (I). 348 MHZ 1H NMR spectra of (I) have been investigated over the temperature range of 25° to -160°C. Two conformation processes affect the 1H NMR spectrum of (I). Iterative force-field calculations on the conformations and conformational interconversion paths of ...

متن کامل

Modern protein force fields behave comparably in molecular dynamics simulations

Several molecular dynamics simulations were performed on three proteins--bovine apo-calbindin D9K, human interleukin-4 R88Q mutant, and domain IIA of bacillus subtilis glucose permease--with each of the AMBER94, CHARMM22, and OPLS-AA force fields as implemented in CHARMM. Structural and dynamic properties such as solvent-accessible surface area, radius of gyration, deviation from their respecti...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

ژورنال

عنوان ژورنال: Science China Physics, Mechanics & Astronomy

سال: 2021

ISSN: ['1869-1927', '1674-7348']

DOI: https://doi.org/10.1007/s11433-021-1739-4